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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 ( Q 0 ) in the first series ( Q 0 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 Q 0 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. [ABSTRACT FROM AUTHOR]