Challenges and strategies for better use of scientific information in the management of coastal estuaries

Numerous studies have concluded that better use of scientific information could improve the quality of coastal and estuarine environmental management. Approaches for effecting such a change include ecosystem-based, integrated, and adaptive management, but such basic re-orientation of estuarine and coastal management has proved difficult to achieve. Even environmental indicators, seemingly straightforward ways of injecting scientific information into decision making, have achieved broad on-the-ground use in relatively few instances—principally the largest estuary management programs. A conceptual framework useful for examining environmental management systems affecting the five PNCERS (Pacific Northwest coastal Ecosystems Regional Study) estuaries conceives of environmental managers, researchers, and interested and affected parties in the public as interacting through the multi-layered institutional arrangements that currently promote the utilization, management, or protection of coastal and estuarine resources. Considerable variation exists in the approach and effectiveness of the region's environmental management organizations. Interaction between science and management in the region appears to be limited to an extent by high transaction costs; a cultural divide between environmental scientists and environmental managers is perceived by members of both groups who work with the PNCERS estuaries as inhibiting communications between them. Mechanisms that both groups identify as useful for improving the flow of information between science and management are little used, perhaps as a result. The two groups have very different patterns of information dissemination and acquisition, and though both chose agency archives and databases as their top methods for disseminating information, neither group relies much on these vehicles for information they seek. Both residents' and practitioners' perceptions of threats to the PNCERS estuaries show patterns of estuary-to-estuary variation. One theme that emerges is that problems associated with poor land management in adjacent uplands are common to most of these estuaries, potentially providing a sense of commonality through which a more regional approach to estuary management could emerge. A common set of estuarine environmental indicators implemented for all estuaries could help instigate such a regional approach, but resource constraints, especially at the local level, will have to be overcome for that to occur. There is currently substantial lack of common vision among coastal practitioners as to the purpose and desirability of indicators, and relatively little experience or knowledge of their use, particularly at the local level. Use of estuarine science in the management of these estuaries appears to be greatest during periods in which the largest programmatic shifts in environmental management approaches occur, an observation consistent with other studies that have concluded that the use of environmental science in environmental management tends to be episodic.     

Data Infrastructures for Estuarine and Coastal Ecological Syntheses

Holistic understanding of estuarine and coastal environments across interacting domains with high-dimensional complexity can profitably be approached through data-centric synthesis studies. Synthesis has been defined as “the inferential process whereby new models are developed from analysis of multiple data sets to explain observed patterns across a range of time and space scales.” Examples include ecological—across ecosystem components or organization levels, spatial—across spatial scales or multiple ecosystems, and temporal—across temporal scales. Though data quantity and volume are increasingly accessible, infrastructures for data sharing, management, and integration remain fractured. Integrating heterogeneous data sets is difficult yet critical. Technological and cultural obstacles hamper finding, accessing, and integrating data to answer scientific and policy questions. To investigate synthesis within the estuarine and coastal science community, we held a workshop at a coastal and estuarine research federation conference and conducted two case studies involving synthesis science. The workshop indicated that data-centric synthesis approaches are valuable for (1) hypothesis testing, (2) baseline monitoring, (3) historical perspectives, and (4) forecasting. Case studies revealed important weaknesses in current data infrastructures and highlighted opportunities for ecological synthesis science. Here, we list requirements for a coastal and estuarine data infrastructure. We model data needs and suggest directions for moving forward. For example, we propose developing community standards, accommodating and integrating big and small data (e.g., sensor feeds and single data sets), and digitizing ‘dark data’ (inaccessible, non-curated, non-archived data potentially destroyed when researchers leave science).     

AnnouncingEstuaries and Coasts, Journal of the Estuarine Research Federation

This is the first issue ofEstuaries and Coasts (ISSN 1559-2723), which continues the Estuarine Research Federation's publication inEstuaries (1978–2005) (ISSN 0160-8347) of scientific reports, reviews, comments, and notes on estuarine and coastal scientific research from around the world. Numbering of volumes ofEstuaries and Coasts continues uninterrupted fromEstuaries since the expanded title was not intended to mark a change in the scope of the journal. It is our hope that the journal will continue to become more international in its coverage, and to include more coastal science than is sometimes associated with the single word nameEstuaries. In addition to the change of the journal's name there is also a new cover design that will change with each issue and highlight an estuary or coast associated with one or more articles in the issue. Another change to the journal is a new column entitled Perspectives in Estuarine and Coastal Science, which is intended to stimulate discussion about emerging topics in estuarine and coastal science. The H. T. Odum Synthesis Essay, initiated in 2005, will be continued on an annual basis.     

Allometric laws and prediction in estuarine and coastal ecology

A theoretical and quantitative framework of first principles would benefit estuarine and coastal ecologists in search of predictions to enhance our understanding and management of marine resources. The Metabolic Theory of Ecology describes a possible unifying theory for ecology, including mechanistically derived equations that predict scaling exponents observed in empirical, allometric relationships from individuals to ecosystems. The controversy surrounding this theory should stimulate our exploration of its potential use in the coastal realm, where questions specific to an applied science may suggest new refinements and derivations, contributing to the overall progress of ecology.     

Impacts of Invasive <Emphasis Type="Italic">Phragmites australis</Emphasis> on Diamondback Terrapin Nesting in Chesapeake Bay

The range expansion of exotic plant species, including the invasive reed Phragmites australis, causes widespread structural and functional changes to coastal ecosystems along the Atlantic and Gulf Coasts of North America. Native estuarine species, such as the diamondback terrapin (Malaclemys terrapin), are at risk of adverse effects from rapid habitat changes due to exotic invasions. Diamondback terrapins currently face population threats including by-catch mortality in crab pots, predation, and habitat loss, and populations may continue to suffer if deleterious plant invasions into preferred nesting habitats are left unchecked. We examined the extent to which Phragmites affects nesting of a breeding population of diamondback terrapins at Fisherman Island National Wildlife Refuge on the eastern shore of Virginia, where Phragmites has recently expanded into known areas of terrapin nesting. With data collected from the 2015 nesting season, we quantified the extent to which Phragmites shading could impact nest incubation temperature and determined how Phragmites density impacts the risk of rhizome invasion into nests. We conclude that Phragmites cover greater than 50% would decrease incubation temperatures of terrapin nests sufficiently to produce predominantly male hatchlings. Phragmites cover had no observed effect on root growth into simulated nests, but cover by other dune plant species explained observed trends in root growth. These results suggest that terrapins may be negatively impacted by Phragmites expansion into open nesting sites. Breeding site fidelity exhibited by terrapins and other estuarine species could limit the ability of their populations to adjust to rapid coastal expansion of invasive plant species.     

Evaluating Adaptive Processes for Conservation and Management of Estuarine and Coastal Resources

This special feature: Genetic Structure and Adaptation in Coastal Ecosystems emphasizes the importance of research focused on population genetic structure and evolutionary change for understanding estuarine and coastal communities. Many studies have examined the effect of environmental gradients on community-level patterns in estuarine habitats; however, relatively little is known about the role of genetically based adaptation (the heritable response to these environmental gradients) in these organisms. This special feature presents 11 studies that use a variety of approaches including ecophysiology, ecological genetics, molecular markers, and patterns of gene expression occurring within these populations. These studies provide examples of the role of genetic diversity and adaptation across a diversity of estuarine and coastal environments, and highlight the temporal and spatial scales at which adaptation impinges upon management. This collection of papers is especially timely, given the increasing importance of understanding and predicting the response to global climate change in order to effectively manage these communities.     

The Runaway Weed: Costs and Failures of Phragmites australis Management in the USA

While public funding of invasive species management has increased substantially in the past decade, there have been few cross-institutional assessments of management programs. We assessed management of Phragmites australis, a problematic invader of coastal habitats, through a cross-institutional economic survey of 285 land managers from US public and private conservation organizations. We found that from 2005 to 2009, these organizations spent >$4.6 million per year on P. australis management, and that 94 % used herbicide to treat a total area of ～80,000 ha. Despite these high expenditures, few organizations accomplished their management objectives. There was no relationship between resources invested in management and management success, and those organizations that endorsed a particular objective were no more likely to achieve it. Our results question the efficacy of current P. australis management strategies and call for future monitoring of biological management outcomes.     

Habitat associations of estuarine species: Comparisons of intertidal mudflat, seagrass (Zostera marina), and oyster (Crassostrea gigas) habitats

The complexity of habitat structure created by aquatic vegetation is an important factor determining the diversity and composition of soft-sediment coastal communities. The introduction of estuarine organisms, such as oysters or other forms of aquaculture, that compete with existing forms of habitat structure, such as seagrass, may affect the availability of important habitat refugia and foraging resources for mobile estuarine fish and decapods. Fish and invertebrate communities were compared between adjacent patches of native seagrass (Zostera marina), nonnative cultured oyster (Crassostrea gigas), and unvegetated mudflat within a northeastern Pacific estuary. The composition of epibenthic meiofauna and small macrofaunal organisms, including known prey of fish and decapods, was significantly related to habitat type. Densities of these epifauna were significantly higher in structured habitat compared to unstructured mudflat. Benthic invertebrate densities were highest in seagrass. Since oyster aquaculture may provide a structural substitute for seagrass being associated with increased density and altered composition of fish and decapod prey resources relative to mudflat, it was hypothesized that this habitat might also alter habitat preferences of foraging fish and decapods. The species composition of fish and decapods was more strongly related to location within the estuary than to habitat, and fish and decapod species composition responded on a larger landscape scale than invertebrate assemblages. Fish and decapod species richness and the size of ecologically and commercially important species, such as Dungeness crab (Cancer magister), English sole (Parophrys vetulus), or lingcod (Ophiodon elongatus), were not significantly related to habitat type.     

Ingress of Brachyuran Crab Post-larvae to the Newport River Estuary

Planktonic larvae of estuarine species often develop in the coastal ocean and return to estuaries using favorable currents. This study investigated spatial distributions of brachyuran crab post-larvae during ingress to the Newport River estuary, North Carolina, USA (34°41′ N, 76°40′ W). Nearshore plankton tows were conducted across the inlet to the estuary. Settlement on passive ‘hog’s hair’ collectors was simultaneously monitored in each of four estuarine channels. Callinectes sapidus density was highest east of the inlet, whereas relative estuarine abundance was higher in western channels. In separate sampling with collectors at coastal and estuarine locations, spatial distributions of post-larvae were consistent through time but differed for C. sapidus, Uca spp., and Pachygrapsus transversus. The diel timing of C. sapidus settlement on collectors was determined at the coast and compared to previous studies of settlement in the estuary. Behavioral responses to environmental cues may alter transport pathways from those predicted by hydrodynamic models.     

Phenotypic Variation Among Invasive <Emphasis Type="Italic">Phragmites australis</Emphasis> Populations Does Not Influence Salinity Tolerance

Phenotypic variation within species can have community- and ecosystem-level effects. Such variation may be particularly important in ecosystem engineers, including many invasive species, because of the strong influence of these species on their surrounding communities and environment. We combined field surveys and glasshouse experiments to investigate phenotypic variation within the invasive common reed, Phragmites australis, among four estuarine source sites along the east coast of North America. Field surveys revealed variation in P. australis height and stem density among source sites. In a glasshouse environment, percent germination of P. australis seeds also varied across source sites. To test the degree to which phenotypic variation in P. australis reflected genetic or environmental differences, we conducted a glasshouse common garden experiment assessing the performance of P. australis seedlings from the four source sites across a salinity gradient. Populations maintained differences in morphology and growth in a common glasshouse environment, indicating a genetic component to the observed phenotypic variation. Despite this variation, experimentally increased porewater salinity consistently reduced P. australis stem density, height, and biomass. Differences in these morphological metrics are important because they are correlated with the impacts of invasive P. australis on the ecological communities it invades. Our results indicate that both colonization and spread of invasive P. australis will be dependent on the environmental and genetic context. Additional research on intraspecific variation in invasive species, particularly ecosystem engineers, will improve assessments of invasion impacts and guide management decisions in estuarine ecosystems.     

Influences of Salinity and Light Availability on Abundance and Distribution of Tidal Freshwater and Oligohaline Submersed Aquatic Vegetation

Submersed aquatic vegetation (SAV) communities have undergone declines worldwide, exposing them to invasions from non-native species. Over the past decade, the invasive species Hydrilla verticillata has been documented in several tributaries of the lower Chesapeake Bay, Virginia. We used annual aerial mapping surveys from 1998 to 2007, integrated with spatial analyses of water quality data, to analyze the patterns and rates of change of a H. verticillata-dominated SAV community and relate them to varying salinity and light conditions. Periods of declining SAV coverage corresponded to periods where salinities exceeded 7 and early growing season (April to May) Secchi depths were <0.4 m. Increases were driven by the expansion of H. verticillata along with several other species into the upper estuary, where some areas experienced an 80% increase in cover. Field investigations revealed H. verticillata dominance to be limited to the upper estuary where total suspended solid concentrations during the early growing season were <15 mg l⁻¹ and salinity remained <3. The effect of poor early growing season water clarity on annual SAV growth highlights the importance of water quality during this critical life stage. Periods of low clarity combined with periodic salinity intrusions may limit the dominance of H. verticillata in these types of estuarine systems. This study shows the importance of the use of these types of biologically relevant episodic events to supplement seasonal habitat requirements and also provides evidence for the potential important role of invasive species in SAV community recovery.     

Contrasting Bacterial Dynamics in Subtropical Estuarine and Coastal Waters

Seasonal succession and composition of both attached and free-living bacterial communities were studied in subtropical estuarine and coastal waters with contrasting hydrographic conditions. A higher abundance of attached bacteria was recovered in the estuarine waters containing high concentrations of dissolved organic carbon (DOC) resulting from the freshwater discharge in the adjacent Pearl River, and Proteobacteria, including ??-, ??-, and ??-groups, predominated the attached community at both stations. Free-living bacterial communities at both stations showed higher diversity and lower seasonality than their attached counterparts, and ??-Proteobacteria accounted for the highest proportion at both stations. Redundancy analysis (RDA) demonstrated that, in addition to the obvious temperature effects, DOC and microphytoplankton (>20???m Chl a) drive the temporal variation of attached bacteria at the estuarine and coastal stations, respectively. On the other hand, picophytoplankton (<2???m Chl a) and dissolved oxygen concentration explained most of the free-living bacterial community succession at the estuarine station, while those at the coastal station were associated with micro- and picoplankton (Chl a fractions of <2 and >20???m). These findings suggest that temperature and bottom?Cup effects play a more important role for the spatial?Ctemporal variations of both attached and free-living bacterial communities in the subtropical estuarine and coastal waters.     

Application of Species Distribution Models to Identify Estuarine Hot Spots for Juvenile Nekton

Modeling the distribution and habitat capacities of key estuarine species can be used to identify hot spots, areas where species density is significantly higher than surrounding areas. This approach would be useful for establishing a baseline for evaluating future environmental scenarios across a landscape. We developed species distribution models for early juvenile life stages of brown shrimp (Farfantepenaeus aztecus), white shrimp (Litopenaeus setiferus), blue crab (Callinectes sapidus), and spotted seatrout (Cynoscion nebulosus) in order to delineate the current coastal hot spots that provide the highest quality habitat conditions for these estuarine-dependent species in Louisiana. Response curves were developed from existing long-term fisheries-independent monitoring data to identify habitat suitability for fragmented marsh landscapes. Response curves were then integrated with spatially explicit input data to generate species distribution models for the coastal region of Louisiana. Using spatial autocorrelation metrics, we detected clusters of suitable habitat across the Louisiana coast, but only 1% of the areas were identified as true hot spots with the highest habitat quality for nekton. The regions identified as hot spots were productive fringing marsh habitats that are considered the most vulnerable to natural and anthropogenic impacts. The species distribution models identify the coastal habitats which currently provide the greatest capacity for key estuarine species and will be used in the Louisiana coastal planning process to evaluate how species distributions may change under various environmental and restoration scenarios.     

Interactions between human communities and estuaries in the Pacific Northwest: Trends and implications for management

This paper explores social, and economic aspects of coastal communities crucial to the management of estuaries in the Pacific Northwest. These aspects include the changing demographics and economies of coastal communities, and the public perceptions, attitudes, and values pertaining to estuarine ecosystems. Information from Willapa Bay and Grays Harbor in Washington and Tillamook, Yaquina, and Coos Bays in Oregon shows that the coastal communities are growing more slowly than the states overall., that the populations are relatively old, and that, although the local economies continue to rely on them, the extractive natural resource industries (fishing, aquaculture, agriculture, forest products) are declining in importance relative to tourism, recreation, and retirement industries. These trends suggest that human uses of the estuaries are changing in character, and altering the management problems. Coastal residents choose to live in these communities to enjoy the views and scenery, to experience rural living, to be near the ocean, and to recreate outdoors. People express coherent perceptions of risks to the estuaries, especially the threats of declining fish habitats, oil spills, shoreline development, invasive species, and logging in upland areas> Residential land values are enhanced by the presence of wetlands and forests and are diminished by the presence of hazardous waste sites. We conclude that, if recent trends in population age structure, income sources, and employment status continue, public attitudes and values will move towards stronger environmental protection. Because ecosystem management involves local public participation and collaboration, estuarine managers will be faced with both increased demands and opportunities.     

An Estuarine Habitat Classification for a Complex Fjordal Island Archipelago

Spatial patterns of estuarine biota suggest that some nearshore ecosystems are functionally linked to interacting processes of the ocean, watershed, and coastal geomorphology. The classification of estuaries can therefore provide important information for distribution studies of nearshore biodiversity. However, many existing classifications are too coarse-scaled to resolve subtle environmental differences that may significantly alter biological structure. We developed an objective three-tier spatially nested classification, then conducted a case study in the Alexander Archipelago of Southeast Alaska, USA, and tested the statistical association of observed biota to changes in estuarine classes. At level 1, the coarsest scale (100–1000’s km²), we used patterns of sea surface temperature and salinity to identify marine domains. At level 2, within each marine domain, fjordal land masses were subdivided into coastal watersheds (10–100’s km²), and 17 estuary classes were identified based on similar marine exposure, river discharge, glacier volume, and snow accumulation. At level 3, the finest scale (1–10’s km²), homogeneous nearshore (depths <10 m) segments were characterized by one of 35 benthic habitat types of the ShoreZone mapping system. The aerial ShoreZone surveys and imagery also provided spatially comprehensive inventories of 19 benthic taxa. These were combined with six anadromous species for a relative measure of estuarine biodiversity. Results suggest that (1) estuaries with similar environmental attributes have similar biological communities, and (2) relative biodiversity increases predictably with increasing habitat complexity, marine exposure, and decreasing freshwater. These results have important implications for the management of ecologically sensitive estuaries.     

Is the Collapse of Mud Shrimp (<Emphasis Type="Italic">Upogebia pugettensis</Emphasis>) Populations Along the Pacific Coast of North America Caused by Outbreaks of a Previously Unknown Bopyrid Isopod Parasite (<Emphasis Type="Italic">Orthione griffenis</Emphasis>)?

A dramatic increase in prevalence of the recently discovered bopyrid isopod parasite, Orthione griffenis, likely introduced in the 1980s from Asia to the Pacific coast of North America, coincided with the 2002 collapse of a population of its burrowing mud shrimp host, Upogebia pugettensis, in Willapa Bay, Washington that had been stable since monitoring began in 1988. An examination of whether O. griffenis infections were sufficient to cause this decline and other recently noted U. pugettensis population collapses in Pacific Coast estuaries was conducted. O. griffenis prevalence was the highest in large reproductive-sized female shrimp and caused an estimated average 68% loss of U. pugettensis reproduction in Yaquina Bay, Oregon over a 5-year period. O. griffenis prevalence fluctuated from year to year, but trends were similar in all estuaries sampled. Uninfected shrimp transplanted back into locations from which they had disappeared acquired the parasite, suggesting that O. griffenis is extremely effective at finding its host even in estuaries with very low host density. Since both U. pugettensis and O. griffenis have pelagic larval stages, their population dynamics are also influenced by coastal nearshore oceanography and estuarine recruitment success. Coastwide lack of estuarine recruitment appears to coincide with declines in density of a co-occurring thalassinid shrimp, Neotrypaea californiensis, but cannot alone explain U. pugettensis population collapses. Although patterns observed to date could be explained by the presence of either a native or introduced parasitic castrator, assumptions of a resilient co-evolved host–parasite relationship do not apply for introduced species, so continued efforts to follow the spatial extent and consequences of the O. griffenis–U. pugettensis host–parasite relationship are warranted.     

Impacts of Coastal Land Use and Shoreline Armoring on Estuarine Ecosystems: an Introduction to a Special Issue

The nearshore land-water interface is an important ecological zone that faces anthropogenic pressure from development in coastal regions throughout the world. Coastal waters and estuaries like Chesapeake Bay receive and process land discharges loaded with anthropogenic nutrients and other pollutants that cause eutrophication, hypoxia, and other damage to shallow-water ecosystems. In addition, shorelines are increasingly armored with bulkhead (seawall), riprap, and other structures to protect human infrastructure against the threats of sea-level rise, storm surge, and erosion. Armoring can further influence estuarine and nearshore marine ecosystem functions by degrading water quality, spreading invasive species, and destroying ecologically valuable habitat. These detrimental effects on ecosystem function have ramifications for ecologically and economically important flora and fauna. This special issue of Estuaries and Coasts explores the interacting effects of coastal land use and shoreline armoring on estuarine and coastal marine ecosystems. The majority of papers focus on the Chesapeake Bay region, USA, where 50 major tributaries and an extensive watershed (~ 167,000 km²), provide an ideal model to examine the impacts of human activities at scales ranging from the local shoreline to the entire watershed. The papers consider the influence of watershed land use and natural versus armored shorelines on ecosystem properties and processes as well as on key natural resources.     

Differential effects of salinity changes on two estuarine fishes,Leiostomus xanthurus andMicropogonias undulatus

Salinity fluctuation has been proposed as an important determinant of estuarine fish distribution. To test this idea, we compared distribution, behavioral preference and physiological sensitivity of two juvenile estuarine fishes, spot (Leiostomus xanthurus) and croaker (Micropogonias undulatus), with respect to salinity change. In field collections, spot: croaker ratios were positively correlated with salinity variation. Subsequent behavioral observations revealed that croaker tend to cross a 10‰ salinity gradient less often than spot. We proposed that energetic costs of salinity adaptation may be higher for croaker, resulting in the observed avoidance behavior. Oxygen consumption rates over rapid salinity fluctuations showed no significant differences in metabolic response between species, although there was some indication that sensitivity changes with fish size. Apparently, juvenile spot and croaker are well-equipped to withstand extreme changes in salinity. We conclude that environmental factors correlated with salinity change may be responsible for distribution differences between these two abundant species.     

The loss of native biodiversity and continuing nonindigenous species introductions in freshwater, estuarine, and wetland communities of Pearl Harbor, Oahu, Hawaiian Islands

The benthic invertebrates and fishes of the estuarine, lower stream areas, and wetlands of Pearl Harbor were sampled from 1997–1998 as a companion study to marine inventories conducted in Pearl Harbor. The first comprehensive assessment of the area found that nonindigenous species comprise the dominant portion of the biota. A total of 191 aquatic species in 8 phyla were identified in the estuarine reaches of Pearl Harbor. Nonindigenous species dominated and comprised 48% of the species, whereas only 33% were native and 19% were cryptogenic. Two new nonindigenous species to Hawaii were found during this study: a species of fang-toothed blenny (Omobranchus ferox) and an estuarine hydrobiid snail (Pyrgophorus cf.coronatus) introduced from the Philippine Islands and the Caribbean, respectively. No single geographic region predominates as a source of aquatic species introductions into the Pearl Harbor area, although more species come from the Americas than other areas. Fifty-seven percent originated from the Americas, 30% from Asia and the Pacific, 5% from Australia/New Zealand, 5% show a world-wide distribution, and fewer than 3% of species originated from Africa. The majority of nonindigenous species appear to arrive from five major sources: intentional and accidental aquarium releases; intentional biocontrol releases; intentional food source releases; ballast water or hull fouling releases; and brought in with airplanes. Non-native species will likely continue to increase in the freshwater and estuarine portions Pearl Harbor because of the wide variety of sources from which introductions take place.     

Long-Term Changes in Water Quality and Productivity in the Patuxent River Estuary: 1985 to 2003

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 O₂ and physical transport of dissolved inorganic nitrogen (DIN) and phosphorus (DIP) using a salt- and water-balance 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 bottom-layer O₂ consumption for upper regions of the estuary. Despite significant reductions in seaward N transport from the middle to lower estuary, chl-a, turbidity, and surface-layer net O₂ 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 chl-a 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.