Coastal water bodies are impacted by watershed alterations, increased population density, modifications to inlets and shorelines, climatic periodicity, and increases in external material loads. Estuaries such as Lake Worth Lagoon (LWL) in south Florida possess all these attributes. The LWL watershed extends from the southeastern portion of Lake Okeechobee through Palm Beach County, where it meets the lagoon. Palm Beach County Department of Environmental Resources Management recognizes the social and ecological importance of the similar to 36 km lagoon and aims to maintain suitable water and habitat quality for all stakeholders. Recent declines and shifts of seagrass distribution along the lagoon prompted a step toward better understanding the water quality patterns of the system. In support of these efforts, this study assessed bathymetry, inflow, flushing, and water quality attributes (chlorophyll a, salinity, total nitrogen, total phosphorus, total suspended solids, turbidity) using data collected along a series of 14 midlagoon stations from 2007 to 2015. Salinity in the North Segment was higher and less variable because of proximity to Palm Beach Inlet. Although concentrations of chlorophyll a, total nitrogen, and total phosphorus correlated with freshwater inflow, turbidity and total suspended solids were not. Fast flushing of the lagoon on a scale of days likely precludes water quality issues common to many estuaries with higher resident times. However, the combination of landscape-scale water management, a shoreline that is almost 70% modified by hard structures, and changes in essential nearshore habitats, introduces new levels of uncertainty to both the understanding and management of LWL. From this study, increased knowledge of relationships among water quality parameters and their spatial and temporal variability in LWL provides points of reference from which targeted studies can be developed to explore links between environmental parameters and responses of key organisms in this unique system.

The South Florida landscape is highly engineered featuring similar to 3380 km of canals, similar to 1225 water control structures, >70 pumping stations, managed wetlands, densely populated coastal watersheds, and impacted estuaries. Landscape scale agricultural and urban modifications require flood control which sometimes results in the release of excess freshwater that potentially damages estuarine ecology. The Central Everglades Planning Project (CEPP) is a partnership between the U.S. Army Corps of Engineers and the South Florida Water Management District focused on restoring natural patterns of freshwater flow to the Everglades and associated estuaries. One of the primary project goals is to reduce deleterious inflows eastward to the St. Lucie Estuary (SLE) and westward to the Caloosahatchee River Estuary (CRE) by diverting freshwater south from Lake Okeechobee. Performance evaluation of the CEPP relies upon integrated modeling which links the watershed engineering projects to estuarine salinities and biotic responses. The objective of this study was to utilize seagrass and oyster models to evaluate the effectiveness of alternative inflow scenarios. There are three different scenarios: the existing condition base (ECB), the future without proposed CEPP projects (FWO) but with other landscape features that could alter freshwater inflows, and alternative 4R (ALT4R) that incorporates a suite of restoration projects including those associated with the CEPP. Each of these inflow scenarios was used to generate daily salinity time series from 1965 to 2005 at multiple locations in the SLE and CRE which were used to run site-specific seagrass and oyster models. The hydrodynamic and ecological effects of freshwater inflow were greater in the SLE compared to the much larger CRE. Predicted densities of oysters (individuals m(-2)) and seagrass (shoots m(-2)) were greater in the wet season (May-Oct) vs. the dry season (Nov-Apr) in both estuaries. Oyster and seagrass densities increased under the ALT4R inflow scenario that mitigated high inflows to the estuaries in the wet season. This result improved environmental conditions while increasing freshwater availability for other parts of the Greater Everglades and the southern estuaries such as Florida Bay and Biscayne Bay. (C) 2014 Elsevier B.V. All rights reserved.

Short- and long-term changes in estuarine biogeochemical and biological attributes are consequences of variations in both the magnitude and composition of freshwater inputs. A common conceptualization of estuaries depicts nutrient loading from coastal watersheds as the stressor that promotes algal biomass, decreases submarine light penetration, and degrades seagrass habitats. Freshwater inflow depresses salinity while simultaneously introducing colored dissolved organic matter (color or CDOM) which greatly reduces estuarine light penetration. This is especially true for sub-tropical estuaries. This study applied a model of the Caloosahatchee River Estuary (CRE) in southwest Florida to explore the relationships between freshwater inflow, nutrient loading, submarine light, and seagrass survival. In two independent model series, the loading of dissolved inorganic nitrogen and phosphorus (DIN and DIP) was reduced by 10%, 20%, 30%, and 50% relative to the base model case from 2002 to 2009 (2922 days). While external nutrient loads were reduced by lowering inflow (Q0) in the first series (Q0 series), reductions were accomplished by decreasing the incoming concentrations of DIN and DIP in the second series (NP Series). The model also was used to explore the partitioning of submarine light extinction due to chlorophyll a, CDOM, and turbidity. Results suggested that attempting to control nutrient loading by decreasing freshwater inflow could have minor effects on water column concentrations but greatly influence submarine light and seagrass biomass. This is because of the relative importance of Q0 to salinity and submarine light. In general, light penetration and seagrass biomass decreased with increased inflow and CDOM. Increased chlorophyll a did account for more submarine light extinction in the lower estuary. The model output was used to help identify desirable levels of inflow, nutrient loading, water quality, salinity, and submarine light for seagrass in the lower CRE. These findings provide information essential to the development of a resource-based approach to improve the management of both freshwater inflow and estuarine biotic resources.

Freshwater pulses to subtropical estuaries often occur on time scales less than 1 week. In particular, introduction of low-level pulses are potentially important during the dry season (November–April) when freshwater is scarce. Determining potential ecological benefits of pulses requires an innovative method of data acquisition at the appropriate spatial and temporal scales. The South Florida Water Management District conducted a pilot study to assess changes in water column attributes with pulse releases to the Caloosahatchee River Estuary (CRE) from January to April 2012. An average inflow of 450 cfs was targeted for a series of freshwater pulses. This study utilized an onboard, flow-through system to record surface water temperature, salinity (S), pH, dissolved oxygen, turbidity, and in situ chlorophyll a (in situ CHL) at 5 s intervals along the 42-km length of the estuary. On each of seven research cruises, the vessel stopped at multiple stations to conduct vertical water column profiles. Salinity increased throughout the CRE as inflow decreased during the study period. Simple correlation and partial least squares regression were used to determine that the downstream locations of the S = 10 isohaline and the maximum CHL concentration (in situ CHLmax) were positively related to inflow. While the in situ CHLmax was located 12–20 km downstream on five of the cruises, it was only a few kilometer from the estuary head on the first (1/12) and last (4/11) dates. It is possible that two circumstances related to freshwater inflow accounted for this pattern. First, water column stratification before January could have stimulated remineralization and primary production. Second, inflow ceased as water temperature increased to 26.0 °C by April to promote algal growth. Further study of the relationships among inflow, water level, flushing time, and CHL is warranted. Future efforts will examine the range of wet season discharge by incorporating a sensor for colored dissolved organic matter to fully connect inflow, salinity, submarine light, and phytoplankton attributes in the CRE.

Oyster beds are disappearing worldwide through a combination of over-harvesting, diseases, and salinity alterations in the coastal zone. Sensitivity of oysters to variable discharge and salinity is particularly acute in small sub-tropical estuaries subject to regulated freshwater releases. South Florida has sub-tropical estuaries where watershed flood control sometimes results in excessive freshwater inflow to estuaries during the wet season (May–Oct) and reduced discharge and increased salinities in the dry season (Nov–Apr). The potential to reserve freshwater accumulated during the wet season could offer the capacity to regulate freshwater at different temporal scales, thus optimizing salinity conditions for estuarine biota. The goal of this study was to use simulation modeling to explore the effects of freshwater inflows and salinity on adult oyster survival in the Caloosahatchee River Estuary (CRE) in southwest Florida. Water managers derived three different freshwater inflow scenarios for the CRE based on historical and modified watershed attributes for the time period of 1965–2000. Three different salinity time series were generated from the inflow scenarios at each of three sites in the lower CRE and used to conduct nine different oyster simulations. Overall, the predicted densities of adult oysters in the upstream site were 3–4 times greater in seasons that experienced reduced freshwater inflow (e.g., increased salinity) with oyster density in the lower estuary much less influenced by the inflows. Potential storage of freshwater reduced the frequency of extreme flows in the wet season and helped to maintain minimum inflow in the dry season near the estuarine mouth. Analyses of inflows indicated that discharges ranging from 0 to 1,500 cfs could promote favorable salinities of 10–25 in the lower CRE depending on wet versus dry season climatic conditions. This range of inflows is similar to that derived in other studies of the CRE and emphasizes the value of simulation models to help prescribe freshwater releases which benefit estuarine biota.

Oyster populations in south Florida estuaries have declined in part through altered salinity driven by anthropogenic changes in freshwater inputs. In particular, the St. Lucie Estuary (SLE) in southeastern Florida has suffered widespread loss of oyster habitat. With efforts underway to improve water quality and oyster habitat in the SLE, the goal of this study was to develop a model to assess ecosystem level impacts of oyster restoration. Phytoplankton and oyster biomass modeling targets were established from observational data collected from 2005 to 2009. Modeled oyster biomass production and filtration fluctuated with temperature, salinity, and total suspended solids from a combination of observational and predicted input functions in 10-year simulations (1998–2007). Model estimates of oyster biomass fluctuated with salinity from near zero after extreme freshwater discharge in 2002–2003 and 2004–2005 to maximum values near 150.0 and 200.0 g C m−2 in spring 1999 and fall 2006. There was potential for algal blooms as turnover time for the phytoplankton standing stock (15.6 days) was faster than water mass turnover (21.0 days). While >1,000 days were required for 50 ha of oyster habitat to filter the entire volume of the estuarine segment, filter time reduced to <20 days with an estimated fivefold increase in net consumption of phytoplankton if the oyster habitat was increased to 300 ha. Re-establishment of biologically desirable salinity envelopes would stabilize oyster survival allowing the possibility for successful habitat restoration to benefit water quality and faunal attributes of the St. Lucie Estuary.

Interactions among geomorphology, circulation, and biogeochemical cycling determine estuary responses to external nutrient loading. In order to better manage watershed nutrient inputs, the goal of this study was to develop seasonal dissolved inorganic nitrogen (DIN) and phosphorus (DIP) budgets for the two estuaries in south Florida, the Caloosahatchee River estuary (CRE) and the St. Lucie Estuary (SLE), from 2002 to 2008. The Land–Ocean Interactions in the Coastal Zone (LOICZ) approach was used to generate water, salt, and DIN and DIP budgets. Results suggested that internal DIN production increases with increased DIN loading to the CRE in the wet season. There were hydrodynamic effects as water column concentrations and ecosystem nutrient processing stabilized in both estuaries as flushing time increased to >10 d. The CRE demonstrated heterotrophy (net ecosystem metabolism or NEM < 0.0) across all wet and dry season budgets. While the SLE was sensitive to DIN loading, system autotrophy (NEM > 0.0) increased significantly with external DIP loading. This included DIP consumption and a bloom of a cyanobacterium (Microcystis aeruginosa) following hurricane-induced discharge to the SLE in 2005. Additionally, while denitrification provided a microbially-mediated N loss pathway for the CRE, this potential was not evident for the SLE where N2 fixation was favored. Disparities between total and inorganic loading ratios suggested that the role of dissolved organic nitrogen (DON) should be assessed for both estuaries. Nutrient budgets indicated that net internal production or consumption of DIN and DIP fluctuated with inter- and intra-annual variations in freshwater inflow, hydrodynamic flushing, and primary production. The results of this study should be included in watershed management plans in order to maintain favorable conditions of external loading relative to internal material cycling in both dry and wet seasons.

Decreased salinity and submarine light associated with hurricanes of 2004–2005 impacted seagrass habitats in the Florida coastal zone. A combination of salinities ≤20 and light attenuation ≥1.5 m−1 resulting from the freshwater discharge in 2005 were among the drivers for a widespread decrease in the coverage and biomass of Syringodium filiforme (manatee grass) in 2006. These observations provided an opportunity to develop and apply a modeling framework to simulate responses of S. filiforme to variable water quality. The framework connects water column variables to field monitoring of seagrass abundance and salinity growth response experiments. The base model was calibrated with macrophyte abundance observed in southern Indian River Lagoon (IRL) from 2002 to 2007 and tested against shoot data from a different time (1997–2002) and nearby location in the IRL. Model shoot biomass (gC m−2) was similar to field observations (r 2 = 0.70) while responding to monthly seasonal fluctuations in salinity and light throughout the 6-year simulations. Field and model results indicated that S. filiforme growth and survival were sensitive to, and increased with, rising salinity throughout 2007. This modeling study emphasizes that discharge, salinity, and submarine light are inter-dependent variables affecting South Florida seagrass habitats on seasonal to inter-annual time scales.

Small estuaries and embayments respond to atmospheric, oceanic, and watershed inputs much faster than large regional estuaries. Simulation models of these ecosystems must approximate the timescales of external inputs versus internal response. Tidal creek ecosystem models indicated that biogeochemical processing rates and magnitude were greater with increased water residence time. In some open estuaries, the absence of benthic filter feeders permits proliferation of phytoplankton if physical transport is not too fast. Model results suggest that reestablishment of estuarine oyster beds leads to phytoplankton removal and improved light transparency. Models of small estuaries allow assessment of linkages among inputs, abiotic drivers, and biogeochemical processing under varying watershed management scenarios.

The monitoring of water colour parameters can provide an important diagnostic tool for the assessment of aquatic ecosystem condition. Remote sensing has long been used to effectively monitor chlorophyll concentrations in open ocean systems; however, operational monitoring in coastal and estuarine areas has been limited because of the inherent complexities of coastal systems, and the coarse spectral and spatial resolutions of available satellite systems. Data were collected using the National Aeronautics and Space Administration (NASA) Advanced Visible-Infrared Imaging Spectrometer (AVIRIS) flown at an altitude of approximately 20 000 m to provide hyperspectral imagery and simulate both MEdium Resolution Imaging Spectrometer (MERIS) and Moderate Resolution Imaging Spectrometer (MODIS) data. AVIRIS data were atmospherically corrected using a radiative transfer modelling approach and analysed using band ratio and linear regression models. Regression analysis was performed with simultaneous field measurements data in the Neuse River Estuary (NRE) and Pamlico Sound on 15 May 2002. Chlorophyll a (Chl a) concentrations were optimally estimated using AVIRIS bands (9.5 nm) centred at 673.6 and 692.7 nm, resulting in a coefficient of determination (R 2) of 0.98. Concentrations of Chromophoric Dissolved Organic Matter (CDOM), Total Suspended Solids (TSS) and Fixed Suspended Solids (FSS) were also estimated, resulting in coefficients of determination of R 2 = 0.90, 0.59 and 0.64, respectively. Ratios of AVIRIS bands centred at or near those corresponding to the MERIS and MODIS sensors indicated that relatively good satellite-based estimates could potentially be derived for water colour constituents at a spatial resolution of 300 and 500 m, respectively.

Tidal creek ecosystems integrate the coastal landscape by linking upland environments to the coastal ocean. These ecosystems feature a combination of sinuous creek beds with wide lateral wetlands interspersed with mud flats and oyster reefs. Previous studies demonstrated negative relationships between habitat quality and indicators of watershed urbanization. However, predicting trends in ecological robustness for a number of irregularly branched tidal ecosystems with different watershed attributes, material inputs, and flushing is a difficult task. This study began to address this task by using a simulation framework to assess water column and sediment ecological processes in two distinct tidal creek ecosystems in South Carolina (Malind Creek versus Okatee Creek). Biogeochemical cycling in these creeks fluctuates with hourly, daily, and seasonal changes in tidal exchange, freshwater and material inputs, and autochthonous primary production. Over 2 years simulation based on 2001–2002 input data an estimated 4–5 times more freshwater entered Okatee Creek than Malind Creek even though Okatee Creek watershed and basin areas are only 2.5X larger. Phytoplankton consumed approximately 70% of all water column dissolved nitrogen annually with autochthonous production the primary source of particulate and dissolved organic carbon (OC) to the sediments. Okatee Creek had approximately 7X the net deposition of OC to the sediments were it combined with sediment microalgal biomass to drive benthic secondary production. Differences in physical transport in salt marsh dominated tidal creeks influence the capacity to process, transform, and sequester introduced materials. Modifications to the simulation model will include improved depth, volume, and tidal exchange for more realistic prediction of effective concentrations. This modeling framework connects watershed and atmospheric material loading to estuarine productivity, has been used to assess differences in ecosystem metabolism with changes in environmental drivers, and provides the foundation for a suite of sub-models to forecast the potential effects of relative sea level rise for a variety of nearshore environments.

Many coastal ecosystems are undergoing anthropogenic stress from large increases in population and urbanization. In many regions changes in freshwater and material inputs to the coastal zone are altering the biogeochemical and biological capacities of ecosystems. Despite increased watershed inputs, large tidal volumes and flushing indicative of macrotidal estuaries can modulate the fate of introduced materials masking some of the symptoms of eutrophication. The Land Use Coastal Ecosystem Study (LU-CES) examined linkages between land use and environmental properties of Malind and Okatee Creeks in South Carolina from 2001 to 2004. The objectives of this particular study were to assess the hydrography of the two macrotidal creek ecosystems, explore differences in dissolved oxygen (DO), and develop a better understanding of the variations in primary and benthic secondary production in southeastern creek ecosystems. Depth, pH, salinity, and DO were reduced and more variable in Malind Creek than in Okatee Creek, although both creeks had strong semidiurnal frequencies in salinity time signatures. While time series analyses of DO saturation in Malind Creek revealed a dominant semidiurnal pattern, Okatee Creek had a distinctly diel DO pattern. The strongly semidiurnal fluctuations in DO and reduced flushing time indicated that biological processes were not fast enough to influence DO in Malind Creek. The Okatee Creek system had a much greater storage volume, a wider marsh, and a dominant 25-h DO frequency. These attributes contributed to an estimated 8–10 times more phytoplankton-based carbon in Okatee Creek and twice the annual benthic production. As expected from their proximity to the upland, low surface area, and high organic content, both ecosystems were net heterotrophic. This fundamental understanding of tidal creek hydrography is being used to help define linkages among differential watershed land uses, flushing characteristics, and levels of biological production in coastal ecosystems of the southeastern United States.

Since the mid 1990s, the Atlantic and Gulf Coast regions have experienced a dramatic increase in the number of hurricane landfalls. In eastern North Carolina alone, eight hurricances have affected the coast in the past 9 years. These storms have exhibited individualistic hydrologic, nutrient, and sediment loading effects and represent a formidable challenge to nutrient management aimed at reducing eutrophication in the Pamlico Sound and its estuarine tributaries. Different rainfall amounts among hurricanes lead to variable freshwater and nutrient discharge and variable nutrient, organic matter, and sediment enrichment. These enrichments differentially affected physical and chemical properties (salinity, water residence time, transparency, stratification, dissolved oxygen), phytoplankton primary production, and phytoplankton community composition. Contrasting ecological responses were accompanied, by changes in nutrient and oxygen cycling, habitat, and higher trophic levels, including different direct effects on fish populations. Floodwaters from the two largest hurricances, Fran (1996) and Floyd (1999), exerted, multi-month to multi-annual effects on hydrology, nutrient loads, productivity, and biotic composition. Relatively low rainfall coastal hurricanes like Isabel (2003) and Ophelia (2005) caused strong vertical mixing and storm surges, but relatively minor hydrologic and nutrient effects. Both hydrologic loading and wind forcing are important drivers and must be integrated with nutrient loading in assessing short-term and long-term ecological effects of these storms. These climatic forcings cannot be managed but should be considered in the development of water quality management strategies for these and other large estuarine ecosystems faced with increasing frequencies and intensities of hurricane activity.

Estuaries integrate atmospheric, watershed, oceanic, and human influences over space and time, Therefore, spatial and temporal patterns in estuarine water-column properties are useful as metrics to evaluate external factors related to internal processes. The National Estuarine Research Reserve monitoring program, including the North Inlet-Winyah Bay complex in South Carolina, provides an ideal setting to track water quality relationships. Our goal was to assess hydrography, chlorophyll a, and particulate and dissolved materials from monitoring data collected at sites from both the salt and estuarine marsh components since 1993-94. Salinity, turbidity, dissolved organic carbon, suspended solids, and chlorophyll a were much greater at the estuarine site, whereas organic nitrogen dominated the total nitrogen pool at both locations. Nitrate was a significant fraction of the total nitrogen pool at the estuarine site but not within the salt marsh. Whereas dissolved organic nitrogen was positively correlated to water temperature, nitrate concentrations were the lowest in the summer, Principal components analysis identified seasonal patterns within the salt marsh for temperature, chlorophyll a, ammonium, suspended solids, and particulate nitrogen. These parameters, grouped together as a primary component, were positively correlated to Spartina alterniflora biomass. In contrast, the estuarine site was more characterized by salinity, pH, and dissolved organic carbon. Although the water-column properties of the salt marsh site reflected a high degree of internal production and remineralization in the summer, patterns at the estuarine site were more likely influenced by seasonal changes in circulation and biogeochemical processing common to coastal plain estuaries.

The underwater light climate is one of the most important determinants of submersed aquatic vegetation. Because of the recent, large-scale, declines in aquatic vegetation, largely attributed to deterioration of the underwater light climate, interest in tools to predict the wax and wane of aquatic macrophyte populations has greatly increased. This paper summarizes two modeling approaches that can be applied to assess impacts of changes in underwater light climate on submersed vegetation. The first, stand-alone, model type focuses on metabolism and biomass formation of submersed freshwater macrophytes with difference in phenologies. This type is illustrated by examples from various sites using models developed for the freshwater macrophytes Hydrilla verticillata (L.f.) Royle (HYDRIL) and Myriophyllum spicatum L. (MILFO), and also by an example ecological risk assessment. The models (HYDRIL and MILFO) track carbon flow through the vegetation in meter-squared (m2) water columns. The models include descriptions of various factors that affect biomass dynamics, such as site-characteristic changes in climate, latitude, light attenuation within the water column, carbon assimilation rate at light saturation, temperature, wintering strategies, grazing and mechanical control (removal of shoot biomass). Simulated biomass, net assimilation and maintenance respiration over a relatively short (1–5 year) period agree well with measured values. The models are, therefore, believed to be suitable for predicting plant community production, growth and survival characteristics over relatively short periods over a large range of sites. The feasibility of using a macrophyte growth model of the HYDRIL type for ecological risk assessment is demonstrated. It is used to evaluate the consequences of management changes in large rivers for the survival of submersed vegetation. The current assessment evaluates the potential impact of increased commercial navigation traffic on the growth of Potamogeton pectinatus L. in Pool 4 of the Upper Mississippi River, U.S.A. In this case, navigational traffic scenarios were translated into suspended solids concentrations and underwater light climate, with the latter being used as inputs into the aquatic plant growth model. Model results demonstrate that the scenario increases in commercial traffic cause minimal decreases in growth and vegetative reproduction. Results indicate that this growth model can be a useful tool in ecological risk assessment, since the required stress-response relationships could be established. The second, integrated, model type focuses on the role of seagrass and other primary producers in estuarine littoral zone material cycling (carbon and nitrogen) at the Goodwin Islands, Virginia, U.S.A. The latter model was used to explore the effects of changes

A year ago, eastern North Carolina was hit over a six‐week period by three large hurricanes. The large‐scale environmental effects began to be recorded as soon as each one subsided; the scientific underpinnings of their longer‐term effects continue to be analyzed. This article details the short and longer‐term effects on the hydrology and biota of Pamlico Sound, the second largest estuary in the United States.

Seagrasses are indicators of ecosystem state because they are sensitive to variations in water composition and clarity resulting from watershed-level impacts. A simulation model designed to study Zostera marina (eelgrass) habitat dynamics in a variable littoral zone environment was used to address the potential ecological responses to eutrophication in lower Chesapeake Bay. The adjacent channel boundary environment is a source of dissolved and particulate materials to the littoral zone. In the simulations, concentrations of key water quality variables in the adjacent estuarine channel boundary were either halved or doubled relative to the base case to investigate light versus nitrogen effects. The role of the seagrass meadow in littoral zone carbon and nitrogen dynamics was evaluated when meadow size was changed in the model. Particulate and dissolved organic carbon accounted for 83% of the submarine light attenuation in the seagrass meadow. In all model runs, the water column concentrations of chlorophyll a and dissolved inorganic nitrogen (DIN) were below the habitat criteria proposed as critical to seagrass survival. Eelgrass community production was carefully regulated by the interactive effects of light, nitrogen, and grazing on epiphyte growth. Increased eelgrass coverage in the littoral zone led to a simulated doubling of ecosystem primary production but reduced the fraction of production by planktonic and sediment microalgae. The simulation model presented here demonstrated the importance of material input from the channel in littoral zone biogeochemical dynamics. Submarine ligh regulated primary production more strongly than inorganic nitrogen concentrations in the model. External DIN concentrations influenced seagrass survival indirectly: enrichment stimulated growth of epiphytes and phytoplankton and promoted shading of the seagras leaf. The model was based upon a unimpacted ecosystem and deteriorated water quality negatively influenced primary production greater than the increases triggered by improved condition. Increased material loading to the littoral zone reduced submarine light availability, increased phytoplankton production, lowered ecosystem production, and reduced subtidal vegetated habitat. This simulation model of the estuarine littoral zone model combines hydrodynamics, biogeochemical sources and sinks, and living resources in order to better understand structure, function, and change in aquatic ecosystems.