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Papers by James Hagy

Estuaries and coasts : journal of the Estuarine Research Federation, 2018

Seasonal responses in estuarine metabolism (primary production, respiration, and net metabolism) ... more Seasonal responses in estuarine metabolism (primary production, respiration, and net metabolism) were examined using two complementary approaches. Total ecosystem metabolism rates were calculated from dissolved oxygen time series using Odum's open water method. Water column rates were calculated from oxygen-based bottle experiments. The study was conducted over a spring-summer season in the Pensacola Bay estuary at a shallow seagrass-dominated site and a deeper bare-bottomed site. Water column integrated gross production rates more than doubled (58.7 to 130.9 mmol O m d) from spring to summer, coinciding with a sharp increase in water column chlorophyll-a, and a decrease in surface salinity. As expected, ecosystem gross production rates were consistently higher than water column rates, but showed a different spring-summer pattern, decreasing at the shoal site from 197 to 168 mmol O m d and sharply increasing at the channel site from 93.4 to 197.4 mmol O m d. The consistency amon...

Estuarine, Coastal and Shelf Science, 2017

San Francisco Bay (SFB), USA, is highly enriched in nitrogen and phosphorus, but has been resista... more San Francisco Bay (SFB), USA, is highly enriched in nitrogen and phosphorus, but has been resistant to the classic symptoms of eutrophication associated with overproduction of phytoplankton. Observations in recent years suggest that this resistance may be weakening, shown by: significant increases of chlorophyll-a (chl-a) and decreases of dissolved oxygen (DO), common occurrences of phytoplankton taxa that can form Harmful Algal Blooms (HAB), and algal toxins in water and mussels reaching levels of concern. As a result, managers now ask: what levels of chl-a in SFB constitute tipping points of phytoplankton biomass beyond which water quality will become degraded, requiring significant nutrient reductions to avoid impairments? We analyzed data for DO, phytoplankton species composition, chl-a, and algal toxins to derive quantitative relationships between three indicators (HAB abundance, toxin concentrations, DO) and chl-a. Quantile regressions relating HAB abundance and DO to chl-a were significant, indicating SFB is at increased risk of adverse HAB and low DO levels if chl-a continues to increase. Conditional probability analysis (CPA) showed chl-a of 13 mg m À3 as a "protective" threshold below which probabilities for exceeding alert levels for HAB abundance and toxins were reduced. This threshold was similar to chl-a of 13e16 mg m À3 that would meet a SFB-wide 80% saturation Water Quality Criterion (WQC) for DO. Higher "at risk" chl-a thresholds from 25 to 40 mg m À3 corresponded to 0.5 probability of exceeding alert levels for HAB abundance, and for DO below a WQC of 5.0 mg L À1 designated for lower South Bay (LSB) and South Bay (SB). We submit these thresholds as a basis to assess eutrophication status of SFB and to inform nutrient management actions. This approach is transferrable to other estuaries to derive chl-a thresholds protective against eutrophication.

Estuaries and Coasts, 2006

The causes and consequences of oxygen depletion in Chesapeake Bay have been the focus of research... more The causes and consequences of oxygen depletion in Chesapeake Bay have been the focus of research, assessment, and policy action over the past several decades. An ongoing scientific re-evaluation of what nutrient load reductions are necessary to meet the water quality goals is needed. While models can provide insights and advice for public policy on load reduction goals, they are caricatures of nature, and it is wise to use independent modeling approaches. In this paper, we describe our simple, biophysically based model that offers a middle ground between statistical models and complex dynamic models. Our model suggests that the target total nitrogen load reduction of 35% will reduce hypoxic volumes by 36-68%, which, on average (53% or 3.4 km 3) is lower than values reported for 1950-1970 (4.2 km 3), and roughly half of the values reported for 1980-1990 (7.2 km 3). By pursuing a simple model construct, we were able to quantify uncertainty to a greater extent than is possible with the more complex numerical models. Yet, by retaining some mechanistic detail we could validate the model against state variables and process rates, an advantage over simple regressions.

Biogeosciences Discussions, 2009

Limnology and Oceanography, 2006

The Choptank and Patuxent tributaries of Chesapeake Bay have become eutrophic over the last 50-10... more The Choptank and Patuxent tributaries of Chesapeake Bay have become eutrophic over the last 50-100 years. Systematic monitoring of nutrient inputs began in ϳ1970, and there have been 2-5-fold increases in nitrogen (N) and phosphorus (P) inputs during 1970-2004 due to sewage discharges, fertilizer applications, atmospheric deposition, and changes in land use. Hydrochemical modeling and land-use yield coefficients suggest that current input rates are 4-20 times higher for N and P than under forested conditions existing 350 yr ago. Sewage is a major cause of increased nutrients in the Patuxent; agricultural inputs dominate in the Choptank. These loading increases have caused three major water-quality problems: (1) increased nutrients, phytoplankton, and turbidity; (2) decreased submerged grasses due to higher turbidity and epiphyton shading; and (3) bottom-water hypoxia due to respiration of excess organic matter. Oxygen in the Patuxent is consistently Ͻ3 mg L Ϫ1 in bottom waters in summer, whereas oxygen in the Choptank has been decreasing for the last 20 yr and is now approaching 3 mg L Ϫ1 in wet years. The low N : P of sewage inputs to the Patuxent results in an N-limited, P-saturated system, whereas the Choptank is primarily limited by N, but with P limitation of phytoplankton during spring river flows. Insufficient action has been taken to improve the water and habitat quality of these estuaries, although reduced eutrophication in dry years suggests that both estuaries will respond to significant decreases in nutrients. Bill Dennison, Denise Breitburg, and two anonymous reviewers provided helpful and timely comments on previous drafts of this manuscript. We thank the EPA Chesapeake Bay Program for financial support and access to the database of the Chesapeake Bay Water Quality Monitoring Program. We acknowledge financial support from Maryland Department of the Environment, NASA Land Cover and Land Use Change Program, and Maryland Department of Natural Resources.

Estuarine, Coastal and Shelf Science, 2005

The often-rapid deposition of phytoplankton to sediments at the end of the spring phytoplankton b... more The often-rapid deposition of phytoplankton to sediments at the end of the spring phytoplankton bloom is an important component of benthic-pelagic coupling in temperate and high latitude estuaries and other aquatic systems. However, quantifying the flux is difficult, particularly in spatially heterogeneous environments. Surficial sediment chlorophyll-a, which can be measured quickly at many locations, has been used effectively by previous studies as an indicator of phytoplankton deposition to estuarine sediments. In this study, surficial sediment chlorophyll-a was quantified in late spring at 20-50 locations throughout Chesapeake Bay for 8 years (1993-2000). A model was developed to estimate chlorophyll-a deposition to sediments using these measurements, while accounting for chlorophyll-a degradation during the time between deposition and sampling. Carbon flux was derived from these estimates via C:chl-a Z 75. Bay-wide, the accumulation of chlorophyll-a on sediments by late spring averaged 171 mg m ÿ2 , from which the chlorophyll-a and carbon sinking fluxes, respectively, were estimated to be 353 mg m ÿ2 and 26.5 gC m ÿ2. These deposition estimates were w50% of estimates based on a sediment trap study in the mid-Bay. During 1993-2000, the highest average chlorophyll-a flux was in the mid-Bay (248 mg m ÿ2), while the lowest was in the lower Bay (191 mg m ÿ2). Winter-spring average river flow was positively correlated with phytoplankton biomass in the lower Bay water column, while phytoplankton biomass in that same region of the Bay was correlated with increased chlorophyll-a deposition to sediments. Responses in other regions of the Bay were less clear and suggested that the concept that nutrient enrichment in high flow years leads to greater phytoplankton deposition to sediments may be an oversimplification. A comparison of the carbon flux associated with the deposition of the spring bloom with annual benthic carbon budgets indicated that the spring bloom did not contribute a disproportionately large fraction of annual carbon inputs to Chesapeake Bay sediments. Regional patterns in chlorophyll-a deposition did not correspond with the strong regional patterns that have been found for plankton net community metabolism during spring.

Estuarine, Coastal and Shelf Science, 2009

We examined the effect of light on water column and benthic fluxes in the Pensacola Bay estuary, ... more We examined the effect of light on water column and benthic fluxes in the Pensacola Bay estuary, a riverdominated system in the northeastern Gulf of Mexico. Measurements were made during the summers of 2003 and 2004 on 16 dates distributed along depth and salinity gradients. Dissolved oxygen fluxes were measured on replicate sediment and water column samples exposed to a gradient of photosynthetically active radiation. Sediment inorganic nutrient (NH 4 þ , NO 3 À , PO 4 3À) fluxes were measured. The response of dissolved oxygen fluxes to variation in light was fit to a photosynthesis-irradiance model and the parameter estimates were used to calculate daily integrated production in the water column and the benthos. The results suggest that shoal environments supported substantial benthic productivity, averaging 13.6 AE 4.7 mmol O 2 m À2 d À1 , whereas channel environments supported low benthic productivity, averaging 0.5 AE 0.3 mmol O 2 m À2 d À1 (AESE). Estimates of baywide microphytobenthic productivity ranged from 8.1 to 16.5 mmol O 2 m À2 d À1 , comprising about 16-32% of total system productivity. Benthic and water column dark respiration averaged 15.2 AE 3.2 and 33.6 AE 3.7 mmol O 2 m À2 d À1 , respectively Inorganic nutrient fluxes were generally low compared to relevant estuarine literature values, and responded minimally to light exposure. Across all stations, nutrient fluxes from sediments to the water column averaged 1.11 AE 0.98 mmol m À2 d À1 for NH 4 þ , 0.58 AE 1.08 mmol m À2 d À1 for NO 3 À , 0.01 AE 0.09 mmol m À2 d À1 for PO 4 3À. The results of this study illustrate how light reaching the sediments is an important modulator of benthic nutrient and oxygen dynamics in shallow estuarine systems.

Estuaries and Coasts, 2007

The relationships between phytoplankton produc~vity, nutrient distributions, and freshwater flow ... more The relationships between phytoplankton produc~vity, nutrient distributions, and freshwater flow were examined in a seasonal study conducted in Escambia Bay, Florida, USA, located in the northeastern Gulf of Mexico. Five sites oriented along the salinity gradient were sampled 24 times over the 28-mo period from 1999 to 2001. Water column profiles of temperature and salinity were measured along with surface chlorophyll and surface inorganic nutrient concentrations. Primary productivity was measured at 2 sites on 11 dates, and estimated for the remaining dates and sites using an empirical regression model relating phytoplankton net production to the product of chlorophyll, euphotic zone depth, and daily solar insolation. Freshwater flow into the system varied markedly over the study period with record low flow during 2000, a flood event in March 2001, and subsequent resttmption of normal flow. Flushing times ranged from 1 d during the flood to 20 d during the drought. Freshwater input strongly affected surface salinity distributions, nutrient flux, chlorophyll, and primary productivity. The flood caused high turbidity and rapid flushing, severely reducing phytoplankton production and biomass accumulation. Following the flood, phytoplankton biomass and productivity sharply increased. Analysis of nutrient distributions suggested Escambia Bay phytoplankton alternated between phosphorus limitation during normal flow and nitrogen limitation during low flow periods. This study found that Escambia Bay is a moderately productive estuary, with an average annual integrated phytoplankton production rate of 290 g C m 2 yr L

Estuaries and Coasts, 2008

We conducted a quantitative assessment of estuarine ecosystem responses to reduced phosphorus and... more We conducted a quantitative assessment of estuarine ecosystem responses to reduced phosphorus and nitrogen loading from sewage treatment facilities and to variability in freshwater flow and nonpoint nutrient inputs to the Patuxent River estuary. We analyzed a 19-year dataset of water quality conditions, nutrient loading, and climatic forcing for three estuarine regions and also computed monthly rates of net production of dissolved O 2 and physical transport of dissolved inorganic nitrogen (DIN) and phosphorus (DIP) using a salt-and waterbalance model. Point-source loading of DIN and DIP to the estuary declined by 40-60% following upgrades to sewage treatment plants and correlated with parallel decreases in DIN and DIP concentrations throughout the Patuxent. Reduced point-source nutrient loading and concentration resulted in declines in phytoplankton chlorophyll-a (chl-a) and light-saturated carbon fixation, as well as in bottomlayer O 2 consumption for upper regions of the estuary. Despite significant reductions in seaward N transport from the middle to lower estuary, chl-a, turbidity, and surfacelayer net O 2 production increased in the lower estuary, especially during summer. This degradation of water quality in the lower estuary appears to be linked to a trend of increasing net inputs of DIN into the estuary from Chesapeake Bay and to above-average river flow during the mid-1990s. In addition, increased abundance of Mnemiopsis leidyi significantly reduced copepod abundance during summer from 1990 to 2002, which favored increases in chla and allowed a shift in total N partitioning from DIN to particulate organic nitrogen. These analyses illustrate (1) the value of long-term monitoring data, (2) the need for regional scale nutrient management that includes integrated estuarine systems, and (3) the potential water quality impacts of altered coastal food webs.

Estuaries, 1998

We measured dissolved and particulate organic carbon (DOC and POC) in samples collected along 13 ... more We measured dissolved and particulate organic carbon (DOC and POC) in samples collected along 13 transects of the salinity gradient of Chesapeake Bay. Biverine DOC and POC end-members averaged 232 + 19 pM and 151 + 53 p.M, respectively, and coastal DOC and POC end-members averaged 172 + 19 pM and 43 f 6 pM, respectively. Within the chlorophyll maximmn, POC accumulated to concentrations 50-150 pM above those expected from conservative mixing and it was significantly correlated with chlorophyll a, hulicating phytoplankton origin. POC accumulated primarily in bottom waters in spring, and primarily in surface waters in summer. Net DOC accumulation (60-120 pM) was observed within and downstream of the chlorophyll maxbnum, prhnarily during spring and summer in both surface and bottom waters, and it also appeared to be derived from phytoplankton. In the turbidity maximmn, there were also net decreases in chlorophyll a (-3 pg 1-l to-22 pg 1-l) and POC concentrations (-2 pM to-89 PM) and transient DOC increases (9-38 pM), primarily in summer. These occurred as freshwater plankton blooms mixed with turbid, low salinity seawater, and we attribute the observed POC and DOC changes to lysis and sedimentation of freshwater plankton. DOC accumulation in both regions of Chesapeake Bay was estimated to be greater than atmospheric or terrestrial organic carbon inputs and was equivalent to-10% of estuarine prhuary production.

Biogeosciences, 2009

The incidence and intensity of hypoxic waters in coastal aquatic ecosystems has been expanding in... more The incidence and intensity of hypoxic waters in coastal aquatic ecosystems has been expanding in recent decades coincident with eutrophication of the coastal zone. Worldwide, there is strong interest in reducing the size and duration of hypoxia in coastal waters, because hypoxia causes negative effects for many organisms and ecosystem processes. Although strategies to reduce hypoxia by decreasing nutrient loading are predicated on the assumption that this action would reverse eutrophication, recent analyses of historical data from European and North American coastal systems suggest little evidence for simple linear response trajectories. We review published parallel time-series data on hypoxia and loading rates for inorganic nutrients and labile organic matter to analyze trajectories of oxygen (O 2) response to nutrient loading. We also assess existing knowledge of physical and ecological factors regulating O 2 in coastal marine waters to facilitate analysis of hypoxia responses to reductions in nutrient (and/or organic matter) inputs. Of the 24 systems identified where concurrent time series of loading and O 2 were available, half displayed relatively clear and direct recoveries following remediation. We explored in detail 5 well-studied systems that have exhibited complex, non-linear responses to variations in loading, including apparent "regime shifts". A summary of these analyses suggests that O 2 conditions improved rapidly and linearly in systems where remediation focused on organic inputs from sewage treatment plants, which were the primary drivers of hypoxia. In larger more open systems where diffuse nutrient loads are more important in fueling O 2 depletion and where

Estuaries and Coasts, 2008

Multi-year nitrogen (N) and phosphorus (P) budgets were developed for the Patuxent River estuary,... more Multi-year nitrogen (N) and phosphorus (P) budgets were developed for the Patuxent River estuary, a seasonally stratified and moderately eutrophic tributary of Chesapeake Bay. Major inputs (point, diffuse, septic, and direct atmospheric) were measured for 13 years during which, large reductions in P and then lesser reductions in N-loading occurred due to wastewater treatment plant improvements. Internal nutrient losses (denitrification and long-term burial of particulate N and P) were measured in tidal marshes and sub-tidal sediments throughout the estuary as were nutrient storage in the water column, sediments, and biota. Nutrient transport between the oligohaline and mesohaline zones and between the Patuxent and Chesapeake Bay was estimated using a salt and water balance model. Several major nutrient recycling terms were directly and indirectly evaluated and compared to new N and P inputs on seasonal and annual timescales. Major findings included: (1) average terrestrial and atmospheric inputs of N and P were very close to the sum of internal losses plus export, suggesting that dominant processes are captured in these budgets; (2) both N and P export were a small fraction (13% and 28%, respectively) of inputs, about half of that expected for N based on water residence times, and almost all exported N and P were in organic forms; (3) the tidal marsh-oligohaline estuary, which by area com-prised~27% of the full estuarine system, removed about 46% and 74% of total annual upland N and P inputs, respectively; (4) recycled N and P were much larger sources of inorganic nutrients than new inputs during warm seasons and were similar in magnitude even during cold seasons; (5) there was clear evidence that major estuarine processes responded rapidly to inter-annual nutrient input variations; (6) historical nutrient input data and nutrient budget data from drought periods indicated that diffuse nutrient sources were dominant and that N loads need to be reduced by about 50% to restore water quality conditions to pre-eutrophic levels.

OCEANS 2009, 2009

The public reporting burden for this collection of information is estimated to average 1 hour per... more The public reporting burden for this collection of information is estimated to average 1 hour per response, including the time for reviewing instructions, searching existing data sources, gathering and maintaining the data needed, and completing and reviewing the collection of information. Send comments regarding this burden estimate or any other aspect of this collection of information, including suggestions for reducing the burden, to the Department of Defense, Executive Services and Communications Directorate (0704-01881. Respondents should be aware that notwithstanding any other provision of law, no person shall be subject to any penalty for failing to comply with a collection of information if it does not display a currently valid OMB control number.

Journal of Geophysical Research: Oceans, 2013

Physical and biogeochemical processes determining the distribution, transport, and fate of nutrie... more Physical and biogeochemical processes determining the distribution, transport, and fate of nutrients delivered by the Mississippi and Atchafalaya river basin (MARB) to the inner Louisiana continental shelf (LCS) were examined using a three-dimensional hydrodynamic model and observations of hydrography, nutrients, and organic carbon collected during 12 cruises. Two aspects of nutrient transport and fate on the inner LCS (<50 m depth) were evaluated: (1) along-shelf and cross-shelf transports were calculated and (2) nutrient sinks and sources were inferred. On average, 47% of the lower Mississippi River freshwater traveled westward on the LCS, but this percentage was reduced during summer when currents reversed to a predominately upcoast direction. Changes from mainly inorganic to organic nutrients were observed at salinity between 20 and 30, and above 30, organic nutrients were the dominant forms. Westward transport of dissolved inorganic nitrogen (DIN) was about 25% of the combined DIN load from the MARB, whereas westward transport of dissolved organic nitrogen (DON) was 2.8-fold larger than the MARB DON load. Different from dissolved inorganic nutrients, for which the rivers were the primary source, the dominant source of organic nutrients was advection from offshore. Overall, the inner LCS was estimated to be a net sink for total nitrogen in the amount of À3.14 mmol N m À2 d À1 and a net sink for total phosphorus in the amount of À0.28 mmol P m À2 d À1. These sinks were approximately 33% and 59% of the total N and P sources, respectively, to the inner LCS.

Environmental Modeling & Assessment, 2015

To improve the description of long-term changes in water quality, a weighted regression approach ... more To improve the description of long-term changes in water quality, a weighted regression approach developed to describe trends in pollutant transport in rivers was adapted to analyze a long-term water quality dataset from Tampa Bay, Florida. The weighted regression approach allows for changes in the relationships between water quality and explanatory variables by using dynamic model parameters and can more clearly resolve the effects of both natural and anthropogenic drivers of ecosystem response. The model resolved changes in chlorophyll-a (chl-a) from 1974 to 2012 at seasonal and multi-annual time scales while considering variation associated with changes in freshwater influence. Separate models were developed for each of the four Bay segments to evaluate spatial differences in patterns of long-term change. Observed trends reflected the known decrease in nitrogen loading to Tampa Bay since the 1970s. Although median chl-a has remained constant in recent decades, model predictions indicated that variation has increased for upper Bay segments and that low biomass events in the lower Bay occur less often. Dynamic relationships between Electronic supplementary material The online version of this article (

Estuaries and Coasts, 2006

Pensacola Bay, Florida, was in the strong northeast quadrant of Hurricane Ivan when it made landf... more Pensacola Bay, Florida, was in the strong northeast quadrant of Hurricane Ivan when it made landfall on September 16, 2004 as a category 3 hurricane on the Saffir-Simpson scale. We present data describing the timeline and maximum height of the storm surge, the extent of flooding of coastal land, and the magnitude of the freshwater inflow pulse that followed the storm. We computed the magnitude of tidal flushing associated with the surge using a tidal prism model. We also evaluated hurricane effects on water quality using water quality surveys conducted 20 and 50 d after the storm, which we compared with a survey 14 d before landfall. We evaluated the scale of hurricane effects relative to normal variability using a 5-yr monthly record. Ivan's 3.5 m storm surge inundated 165 km 2 of land, increasing the surface area of Pensacola Bay by 50% and its volume by 230%. The model suggests that 60% of the Bay's volume was flushed, initially increasing the average salinity of Bay waters from 23 to 30 and lowering nutrient and chlorophyll a concentrations. Additional computations suggest that wind forcing was sufficient to completely mix the water column during the storm. Freshwater discharge from the largest river increased twentyfold during the subsequent 4 d, stimulating a modest phytoplankton bloom (chlorophyll up to 18 mg l 21) and maintaining hypoxia for several months. Although the immediate physical perturbation was extreme, the water quality effects that persisted beyond the first several days were within the normal range of variability for this system. In terms of water quality and phytoplankton productivity effects, this ecosystem appears to be quite resilient in the face of a severe hurricane effect.

Journal of Environment Quality, 2004

The environmental fate of herbicides in estuaries is poorly underfate of these chemicals in the t... more The environmental fate of herbicides in estuaries is poorly underfate of these chemicals in the tidal portion of the rivers. stood. Estuarine physical transport processes and the episodic nature of herbicide release into surface waters complicate interpretation of Herbicides have been found to harm the lower levels water concentration measurements and allocation of sources. Water of the estuarine food chain either directly (Lytle and concentrations of herbicides and two triazine degradation products

Estuaries, 2000

A box model based on salinity distributions and freshwater inflow measurements was developed and ... more A box model based on salinity distributions and freshwater inflow measurements was developed and used to estimate net non-tidal physical circulation and hydraulic residence times for Patuxent River estuary, Maryland, a tributary estuary of Chesapeake Bay. The box model relaxes the usual assumption that salinity is at steady-state, an important improvement over previous box model studies, yet it remains simple enough to have broad appeal. Average monthly 2-dimensional net non-tidal circulation and residence times for 1986-1995 are estimated and related to river flow and salt water inflow as estimated by the box model. An important result is that advective exchange at the estuary mouth was not correlated with Patuxent River flow, most likely due to effects of offshore salinity changes in Chesapeake Bay. The median residence time for freshwater entering at the head of the estuary was 68 d and decreased hyperbolically with increasing river flow to 30 d during high flow. Estimates of residence times for down-estuary points of origin showed that, from the head of the estuary to its mouth, control of flushing changed from primarily river flow to other factors regulating the intensity of gravitational circulation.

Estuaries and coasts : journal of the Estuarine Research Federation, 2018

Seasonal responses in estuarine metabolism (primary production, respiration, and net metabolism) ... more Seasonal responses in estuarine metabolism (primary production, respiration, and net metabolism) were examined using two complementary approaches. Total ecosystem metabolism rates were calculated from dissolved oxygen time series using Odum's open water method. Water column rates were calculated from oxygen-based bottle experiments. The study was conducted over a spring-summer season in the Pensacola Bay estuary at a shallow seagrass-dominated site and a deeper bare-bottomed site. Water column integrated gross production rates more than doubled (58.7 to 130.9 mmol O m d) from spring to summer, coinciding with a sharp increase in water column chlorophyll-a, and a decrease in surface salinity. As expected, ecosystem gross production rates were consistently higher than water column rates, but showed a different spring-summer pattern, decreasing at the shoal site from 197 to 168 mmol O m d and sharply increasing at the channel site from 93.4 to 197.4 mmol O m d. The consistency amon...

Estuarine, Coastal and Shelf Science, 2017

San Francisco Bay (SFB), USA, is highly enriched in nitrogen and phosphorus, but has been resista... more San Francisco Bay (SFB), USA, is highly enriched in nitrogen and phosphorus, but has been resistant to the classic symptoms of eutrophication associated with overproduction of phytoplankton. Observations in recent years suggest that this resistance may be weakening, shown by: significant increases of chlorophyll-a (chl-a) and decreases of dissolved oxygen (DO), common occurrences of phytoplankton taxa that can form Harmful Algal Blooms (HAB), and algal toxins in water and mussels reaching levels of concern. As a result, managers now ask: what levels of chl-a in SFB constitute tipping points of phytoplankton biomass beyond which water quality will become degraded, requiring significant nutrient reductions to avoid impairments? We analyzed data for DO, phytoplankton species composition, chl-a, and algal toxins to derive quantitative relationships between three indicators (HAB abundance, toxin concentrations, DO) and chl-a. Quantile regressions relating HAB abundance and DO to chl-a were significant, indicating SFB is at increased risk of adverse HAB and low DO levels if chl-a continues to increase. Conditional probability analysis (CPA) showed chl-a of 13 mg m À3 as a "protective" threshold below which probabilities for exceeding alert levels for HAB abundance and toxins were reduced. This threshold was similar to chl-a of 13e16 mg m À3 that would meet a SFB-wide 80% saturation Water Quality Criterion (WQC) for DO. Higher "at risk" chl-a thresholds from 25 to 40 mg m À3 corresponded to 0.5 probability of exceeding alert levels for HAB abundance, and for DO below a WQC of 5.0 mg L À1 designated for lower South Bay (LSB) and South Bay (SB). We submit these thresholds as a basis to assess eutrophication status of SFB and to inform nutrient management actions. This approach is transferrable to other estuaries to derive chl-a thresholds protective against eutrophication.

Estuaries and Coasts, 2006

The causes and consequences of oxygen depletion in Chesapeake Bay have been the focus of research... more The causes and consequences of oxygen depletion in Chesapeake Bay have been the focus of research, assessment, and policy action over the past several decades. An ongoing scientific re-evaluation of what nutrient load reductions are necessary to meet the water quality goals is needed. While models can provide insights and advice for public policy on load reduction goals, they are caricatures of nature, and it is wise to use independent modeling approaches. In this paper, we describe our simple, biophysically based model that offers a middle ground between statistical models and complex dynamic models. Our model suggests that the target total nitrogen load reduction of 35% will reduce hypoxic volumes by 36-68%, which, on average (53% or 3.4 km 3) is lower than values reported for 1950-1970 (4.2 km 3), and roughly half of the values reported for 1980-1990 (7.2 km 3). By pursuing a simple model construct, we were able to quantify uncertainty to a greater extent than is possible with the more complex numerical models. Yet, by retaining some mechanistic detail we could validate the model against state variables and process rates, an advantage over simple regressions.

Biogeosciences Discussions, 2009

Limnology and Oceanography, 2006

The Choptank and Patuxent tributaries of Chesapeake Bay have become eutrophic over the last 50-10... more The Choptank and Patuxent tributaries of Chesapeake Bay have become eutrophic over the last 50-100 years. Systematic monitoring of nutrient inputs began in ϳ1970, and there have been 2-5-fold increases in nitrogen (N) and phosphorus (P) inputs during 1970-2004 due to sewage discharges, fertilizer applications, atmospheric deposition, and changes in land use. Hydrochemical modeling and land-use yield coefficients suggest that current input rates are 4-20 times higher for N and P than under forested conditions existing 350 yr ago. Sewage is a major cause of increased nutrients in the Patuxent; agricultural inputs dominate in the Choptank. These loading increases have caused three major water-quality problems: (1) increased nutrients, phytoplankton, and turbidity; (2) decreased submerged grasses due to higher turbidity and epiphyton shading; and (3) bottom-water hypoxia due to respiration of excess organic matter. Oxygen in the Patuxent is consistently Ͻ3 mg L Ϫ1 in bottom waters in summer, whereas oxygen in the Choptank has been decreasing for the last 20 yr and is now approaching 3 mg L Ϫ1 in wet years. The low N : P of sewage inputs to the Patuxent results in an N-limited, P-saturated system, whereas the Choptank is primarily limited by N, but with P limitation of phytoplankton during spring river flows. Insufficient action has been taken to improve the water and habitat quality of these estuaries, although reduced eutrophication in dry years suggests that both estuaries will respond to significant decreases in nutrients. Bill Dennison, Denise Breitburg, and two anonymous reviewers provided helpful and timely comments on previous drafts of this manuscript. We thank the EPA Chesapeake Bay Program for financial support and access to the database of the Chesapeake Bay Water Quality Monitoring Program. We acknowledge financial support from Maryland Department of the Environment, NASA Land Cover and Land Use Change Program, and Maryland Department of Natural Resources.

Estuarine, Coastal and Shelf Science, 2005

The often-rapid deposition of phytoplankton to sediments at the end of the spring phytoplankton b... more The often-rapid deposition of phytoplankton to sediments at the end of the spring phytoplankton bloom is an important component of benthic-pelagic coupling in temperate and high latitude estuaries and other aquatic systems. However, quantifying the flux is difficult, particularly in spatially heterogeneous environments. Surficial sediment chlorophyll-a, which can be measured quickly at many locations, has been used effectively by previous studies as an indicator of phytoplankton deposition to estuarine sediments. In this study, surficial sediment chlorophyll-a was quantified in late spring at 20-50 locations throughout Chesapeake Bay for 8 years (1993-2000). A model was developed to estimate chlorophyll-a deposition to sediments using these measurements, while accounting for chlorophyll-a degradation during the time between deposition and sampling. Carbon flux was derived from these estimates via C:chl-a Z 75. Bay-wide, the accumulation of chlorophyll-a on sediments by late spring averaged 171 mg m ÿ2 , from which the chlorophyll-a and carbon sinking fluxes, respectively, were estimated to be 353 mg m ÿ2 and 26.5 gC m ÿ2. These deposition estimates were w50% of estimates based on a sediment trap study in the mid-Bay. During 1993-2000, the highest average chlorophyll-a flux was in the mid-Bay (248 mg m ÿ2), while the lowest was in the lower Bay (191 mg m ÿ2). Winter-spring average river flow was positively correlated with phytoplankton biomass in the lower Bay water column, while phytoplankton biomass in that same region of the Bay was correlated with increased chlorophyll-a deposition to sediments. Responses in other regions of the Bay were less clear and suggested that the concept that nutrient enrichment in high flow years leads to greater phytoplankton deposition to sediments may be an oversimplification. A comparison of the carbon flux associated with the deposition of the spring bloom with annual benthic carbon budgets indicated that the spring bloom did not contribute a disproportionately large fraction of annual carbon inputs to Chesapeake Bay sediments. Regional patterns in chlorophyll-a deposition did not correspond with the strong regional patterns that have been found for plankton net community metabolism during spring.

Estuarine, Coastal and Shelf Science, 2009

We examined the effect of light on water column and benthic fluxes in the Pensacola Bay estuary, ... more We examined the effect of light on water column and benthic fluxes in the Pensacola Bay estuary, a riverdominated system in the northeastern Gulf of Mexico. Measurements were made during the summers of 2003 and 2004 on 16 dates distributed along depth and salinity gradients. Dissolved oxygen fluxes were measured on replicate sediment and water column samples exposed to a gradient of photosynthetically active radiation. Sediment inorganic nutrient (NH 4 þ , NO 3 À , PO 4 3À) fluxes were measured. The response of dissolved oxygen fluxes to variation in light was fit to a photosynthesis-irradiance model and the parameter estimates were used to calculate daily integrated production in the water column and the benthos. The results suggest that shoal environments supported substantial benthic productivity, averaging 13.6 AE 4.7 mmol O 2 m À2 d À1 , whereas channel environments supported low benthic productivity, averaging 0.5 AE 0.3 mmol O 2 m À2 d À1 (AESE). Estimates of baywide microphytobenthic productivity ranged from 8.1 to 16.5 mmol O 2 m À2 d À1 , comprising about 16-32% of total system productivity. Benthic and water column dark respiration averaged 15.2 AE 3.2 and 33.6 AE 3.7 mmol O 2 m À2 d À1 , respectively Inorganic nutrient fluxes were generally low compared to relevant estuarine literature values, and responded minimally to light exposure. Across all stations, nutrient fluxes from sediments to the water column averaged 1.11 AE 0.98 mmol m À2 d À1 for NH 4 þ , 0.58 AE 1.08 mmol m À2 d À1 for NO 3 À , 0.01 AE 0.09 mmol m À2 d À1 for PO 4 3À. The results of this study illustrate how light reaching the sediments is an important modulator of benthic nutrient and oxygen dynamics in shallow estuarine systems.

Estuaries and Coasts, 2007

The relationships between phytoplankton produc~vity, nutrient distributions, and freshwater flow ... more The relationships between phytoplankton produc~vity, nutrient distributions, and freshwater flow were examined in a seasonal study conducted in Escambia Bay, Florida, USA, located in the northeastern Gulf of Mexico. Five sites oriented along the salinity gradient were sampled 24 times over the 28-mo period from 1999 to 2001. Water column profiles of temperature and salinity were measured along with surface chlorophyll and surface inorganic nutrient concentrations. Primary productivity was measured at 2 sites on 11 dates, and estimated for the remaining dates and sites using an empirical regression model relating phytoplankton net production to the product of chlorophyll, euphotic zone depth, and daily solar insolation. Freshwater flow into the system varied markedly over the study period with record low flow during 2000, a flood event in March 2001, and subsequent resttmption of normal flow. Flushing times ranged from 1 d during the flood to 20 d during the drought. Freshwater input strongly affected surface salinity distributions, nutrient flux, chlorophyll, and primary productivity. The flood caused high turbidity and rapid flushing, severely reducing phytoplankton production and biomass accumulation. Following the flood, phytoplankton biomass and productivity sharply increased. Analysis of nutrient distributions suggested Escambia Bay phytoplankton alternated between phosphorus limitation during normal flow and nitrogen limitation during low flow periods. This study found that Escambia Bay is a moderately productive estuary, with an average annual integrated phytoplankton production rate of 290 g C m 2 yr L

Estuaries and Coasts, 2008

We conducted a quantitative assessment of estuarine ecosystem responses to reduced phosphorus and... more We conducted a quantitative assessment of estuarine ecosystem responses to reduced phosphorus and nitrogen loading from sewage treatment facilities and to variability in freshwater flow and nonpoint nutrient inputs to the Patuxent River estuary. We analyzed a 19-year dataset of water quality conditions, nutrient loading, and climatic forcing for three estuarine regions and also computed monthly rates of net production of dissolved O 2 and physical transport of dissolved inorganic nitrogen (DIN) and phosphorus (DIP) using a salt-and waterbalance model. Point-source loading of DIN and DIP to the estuary declined by 40-60% following upgrades to sewage treatment plants and correlated with parallel decreases in DIN and DIP concentrations throughout the Patuxent. Reduced point-source nutrient loading and concentration resulted in declines in phytoplankton chlorophyll-a (chl-a) and light-saturated carbon fixation, as well as in bottomlayer O 2 consumption for upper regions of the estuary. Despite significant reductions in seaward N transport from the middle to lower estuary, chl-a, turbidity, and surfacelayer net O 2 production increased in the lower estuary, especially during summer. This degradation of water quality in the lower estuary appears to be linked to a trend of increasing net inputs of DIN into the estuary from Chesapeake Bay and to above-average river flow during the mid-1990s. In addition, increased abundance of Mnemiopsis leidyi significantly reduced copepod abundance during summer from 1990 to 2002, which favored increases in chla and allowed a shift in total N partitioning from DIN to particulate organic nitrogen. These analyses illustrate (1) the value of long-term monitoring data, (2) the need for regional scale nutrient management that includes integrated estuarine systems, and (3) the potential water quality impacts of altered coastal food webs.

Estuaries, 1998

We measured dissolved and particulate organic carbon (DOC and POC) in samples collected along 13 ... more We measured dissolved and particulate organic carbon (DOC and POC) in samples collected along 13 transects of the salinity gradient of Chesapeake Bay. Biverine DOC and POC end-members averaged 232 + 19 pM and 151 + 53 p.M, respectively, and coastal DOC and POC end-members averaged 172 + 19 pM and 43 f 6 pM, respectively. Within the chlorophyll maximmn, POC accumulated to concentrations 50-150 pM above those expected from conservative mixing and it was significantly correlated with chlorophyll a, hulicating phytoplankton origin. POC accumulated primarily in bottom waters in spring, and primarily in surface waters in summer. Net DOC accumulation (60-120 pM) was observed within and downstream of the chlorophyll maxbnum, prhnarily during spring and summer in both surface and bottom waters, and it also appeared to be derived from phytoplankton. In the turbidity maximmn, there were also net decreases in chlorophyll a (-3 pg 1-l to-22 pg 1-l) and POC concentrations (-2 pM to-89 PM) and transient DOC increases (9-38 pM), primarily in summer. These occurred as freshwater plankton blooms mixed with turbid, low salinity seawater, and we attribute the observed POC and DOC changes to lysis and sedimentation of freshwater plankton. DOC accumulation in both regions of Chesapeake Bay was estimated to be greater than atmospheric or terrestrial organic carbon inputs and was equivalent to-10% of estuarine prhuary production.

Biogeosciences, 2009

The incidence and intensity of hypoxic waters in coastal aquatic ecosystems has been expanding in... more The incidence and intensity of hypoxic waters in coastal aquatic ecosystems has been expanding in recent decades coincident with eutrophication of the coastal zone. Worldwide, there is strong interest in reducing the size and duration of hypoxia in coastal waters, because hypoxia causes negative effects for many organisms and ecosystem processes. Although strategies to reduce hypoxia by decreasing nutrient loading are predicated on the assumption that this action would reverse eutrophication, recent analyses of historical data from European and North American coastal systems suggest little evidence for simple linear response trajectories. We review published parallel time-series data on hypoxia and loading rates for inorganic nutrients and labile organic matter to analyze trajectories of oxygen (O 2) response to nutrient loading. We also assess existing knowledge of physical and ecological factors regulating O 2 in coastal marine waters to facilitate analysis of hypoxia responses to reductions in nutrient (and/or organic matter) inputs. Of the 24 systems identified where concurrent time series of loading and O 2 were available, half displayed relatively clear and direct recoveries following remediation. We explored in detail 5 well-studied systems that have exhibited complex, non-linear responses to variations in loading, including apparent "regime shifts". A summary of these analyses suggests that O 2 conditions improved rapidly and linearly in systems where remediation focused on organic inputs from sewage treatment plants, which were the primary drivers of hypoxia. In larger more open systems where diffuse nutrient loads are more important in fueling O 2 depletion and where

Estuaries and Coasts, 2008

Multi-year nitrogen (N) and phosphorus (P) budgets were developed for the Patuxent River estuary,... more Multi-year nitrogen (N) and phosphorus (P) budgets were developed for the Patuxent River estuary, a seasonally stratified and moderately eutrophic tributary of Chesapeake Bay. Major inputs (point, diffuse, septic, and direct atmospheric) were measured for 13 years during which, large reductions in P and then lesser reductions in N-loading occurred due to wastewater treatment plant improvements. Internal nutrient losses (denitrification and long-term burial of particulate N and P) were measured in tidal marshes and sub-tidal sediments throughout the estuary as were nutrient storage in the water column, sediments, and biota. Nutrient transport between the oligohaline and mesohaline zones and between the Patuxent and Chesapeake Bay was estimated using a salt and water balance model. Several major nutrient recycling terms were directly and indirectly evaluated and compared to new N and P inputs on seasonal and annual timescales. Major findings included: (1) average terrestrial and atmospheric inputs of N and P were very close to the sum of internal losses plus export, suggesting that dominant processes are captured in these budgets; (2) both N and P export were a small fraction (13% and 28%, respectively) of inputs, about half of that expected for N based on water residence times, and almost all exported N and P were in organic forms; (3) the tidal marsh-oligohaline estuary, which by area com-prised~27% of the full estuarine system, removed about 46% and 74% of total annual upland N and P inputs, respectively; (4) recycled N and P were much larger sources of inorganic nutrients than new inputs during warm seasons and were similar in magnitude even during cold seasons; (5) there was clear evidence that major estuarine processes responded rapidly to inter-annual nutrient input variations; (6) historical nutrient input data and nutrient budget data from drought periods indicated that diffuse nutrient sources were dominant and that N loads need to be reduced by about 50% to restore water quality conditions to pre-eutrophic levels.

OCEANS 2009, 2009

The public reporting burden for this collection of information is estimated to average 1 hour per... more The public reporting burden for this collection of information is estimated to average 1 hour per response, including the time for reviewing instructions, searching existing data sources, gathering and maintaining the data needed, and completing and reviewing the collection of information. Send comments regarding this burden estimate or any other aspect of this collection of information, including suggestions for reducing the burden, to the Department of Defense, Executive Services and Communications Directorate (0704-01881. Respondents should be aware that notwithstanding any other provision of law, no person shall be subject to any penalty for failing to comply with a collection of information if it does not display a currently valid OMB control number.

Journal of Geophysical Research: Oceans, 2013

Physical and biogeochemical processes determining the distribution, transport, and fate of nutrie... more Physical and biogeochemical processes determining the distribution, transport, and fate of nutrients delivered by the Mississippi and Atchafalaya river basin (MARB) to the inner Louisiana continental shelf (LCS) were examined using a three-dimensional hydrodynamic model and observations of hydrography, nutrients, and organic carbon collected during 12 cruises. Two aspects of nutrient transport and fate on the inner LCS (<50 m depth) were evaluated: (1) along-shelf and cross-shelf transports were calculated and (2) nutrient sinks and sources were inferred. On average, 47% of the lower Mississippi River freshwater traveled westward on the LCS, but this percentage was reduced during summer when currents reversed to a predominately upcoast direction. Changes from mainly inorganic to organic nutrients were observed at salinity between 20 and 30, and above 30, organic nutrients were the dominant forms. Westward transport of dissolved inorganic nitrogen (DIN) was about 25% of the combined DIN load from the MARB, whereas westward transport of dissolved organic nitrogen (DON) was 2.8-fold larger than the MARB DON load. Different from dissolved inorganic nutrients, for which the rivers were the primary source, the dominant source of organic nutrients was advection from offshore. Overall, the inner LCS was estimated to be a net sink for total nitrogen in the amount of À3.14 mmol N m À2 d À1 and a net sink for total phosphorus in the amount of À0.28 mmol P m À2 d À1. These sinks were approximately 33% and 59% of the total N and P sources, respectively, to the inner LCS.

Environmental Modeling & Assessment, 2015

To improve the description of long-term changes in water quality, a weighted regression approach ... more To improve the description of long-term changes in water quality, a weighted regression approach developed to describe trends in pollutant transport in rivers was adapted to analyze a long-term water quality dataset from Tampa Bay, Florida. The weighted regression approach allows for changes in the relationships between water quality and explanatory variables by using dynamic model parameters and can more clearly resolve the effects of both natural and anthropogenic drivers of ecosystem response. The model resolved changes in chlorophyll-a (chl-a) from 1974 to 2012 at seasonal and multi-annual time scales while considering variation associated with changes in freshwater influence. Separate models were developed for each of the four Bay segments to evaluate spatial differences in patterns of long-term change. Observed trends reflected the known decrease in nitrogen loading to Tampa Bay since the 1970s. Although median chl-a has remained constant in recent decades, model predictions indicated that variation has increased for upper Bay segments and that low biomass events in the lower Bay occur less often. Dynamic relationships between Electronic supplementary material The online version of this article (

Estuaries and Coasts, 2006

Pensacola Bay, Florida, was in the strong northeast quadrant of Hurricane Ivan when it made landf... more Pensacola Bay, Florida, was in the strong northeast quadrant of Hurricane Ivan when it made landfall on September 16, 2004 as a category 3 hurricane on the Saffir-Simpson scale. We present data describing the timeline and maximum height of the storm surge, the extent of flooding of coastal land, and the magnitude of the freshwater inflow pulse that followed the storm. We computed the magnitude of tidal flushing associated with the surge using a tidal prism model. We also evaluated hurricane effects on water quality using water quality surveys conducted 20 and 50 d after the storm, which we compared with a survey 14 d before landfall. We evaluated the scale of hurricane effects relative to normal variability using a 5-yr monthly record. Ivan's 3.5 m storm surge inundated 165 km 2 of land, increasing the surface area of Pensacola Bay by 50% and its volume by 230%. The model suggests that 60% of the Bay's volume was flushed, initially increasing the average salinity of Bay waters from 23 to 30 and lowering nutrient and chlorophyll a concentrations. Additional computations suggest that wind forcing was sufficient to completely mix the water column during the storm. Freshwater discharge from the largest river increased twentyfold during the subsequent 4 d, stimulating a modest phytoplankton bloom (chlorophyll up to 18 mg l 21) and maintaining hypoxia for several months. Although the immediate physical perturbation was extreme, the water quality effects that persisted beyond the first several days were within the normal range of variability for this system. In terms of water quality and phytoplankton productivity effects, this ecosystem appears to be quite resilient in the face of a severe hurricane effect.

Journal of Environment Quality, 2004

The environmental fate of herbicides in estuaries is poorly underfate of these chemicals in the t... more The environmental fate of herbicides in estuaries is poorly underfate of these chemicals in the tidal portion of the rivers. stood. Estuarine physical transport processes and the episodic nature of herbicide release into surface waters complicate interpretation of Herbicides have been found to harm the lower levels water concentration measurements and allocation of sources. Water of the estuarine food chain either directly (Lytle and concentrations of herbicides and two triazine degradation products

Estuaries, 2000

A box model based on salinity distributions and freshwater inflow measurements was developed and ... more A box model based on salinity distributions and freshwater inflow measurements was developed and used to estimate net non-tidal physical circulation and hydraulic residence times for Patuxent River estuary, Maryland, a tributary estuary of Chesapeake Bay. The box model relaxes the usual assumption that salinity is at steady-state, an important improvement over previous box model studies, yet it remains simple enough to have broad appeal. Average monthly 2-dimensional net non-tidal circulation and residence times for 1986-1995 are estimated and related to river flow and salt water inflow as estimated by the box model. An important result is that advective exchange at the estuary mouth was not correlated with Patuxent River flow, most likely due to effects of offshore salinity changes in Chesapeake Bay. The median residence time for freshwater entering at the head of the estuary was 68 d and decreased hyperbolically with increasing river flow to 30 d during high flow. Estimates of residence times for down-estuary points of origin showed that, from the head of the estuary to its mouth, control of flushing changed from primarily river flow to other factors regulating the intensity of gravitational circulation.