Long Island Sound (LIS) is a seasonally hypoxic estuary that receives sewage effluent and nonpoint source nutrient pollution from New York City, Long Island, and the Housatonic, Connecticut, and Thames Rivers in Connecticut. Data collected on 9 research cruises during the summers of 2009 and 2010 in western LIS revealed that organic matter associated with surface water phytoplankton production explained about half the variability (p<0.01) in total community respiration in surface waters. Phytoplankton biomass and particulate organic carbon concentrations explained 66% (p < 0.001) and 72% (p<0.01) of the variability in bacterial abundances, respectively, suggesting bacteria were associated with organic matter from phytoplankton production. Bacterial net production (BNP) seemed to be controlled by temperature (r = 0.49, p < 0.01). However, BNP did not correlate with respiration, DO, or organic matter concentrations. Bacterial abundances explained a portion of bottom water oxygen demand in the <20-¶æm fraction (r = 0.50, p <0.01). Furthermore, bottom water column respiration of particles < 20-¶æm accounted for 41% of the variability in bottom water dissolved oxygen (DO) concentrations (r = -0.64, p = 0.06). Despite 20% reductions in nitrogen-loadings to LIS in the past 17 years, the extent, duration, and volume of hypoxia have not significantly declined. A retrospective analysis of 15 years of chemical, biological, and hydrographic monitoring data from 9 stations along the central axis of LIS produced by the Connecticut Department of Environmental Protection (CTDEP) suggested that policies targeting nutrient reductions from sewage effluent have introduced excess phosphate and induced nitrogen-limitation for phytoplankton communities, particularly in western LIS. However, rather than an overall decrease in phytoplanktonic biomass, these changes in nutrient stoichiometry have caused a long-term shift in community composition. In particular, although diatoms still make up the majority of phytoplankton biomass, they have decreased in abundance in favor of nondiatom species, mainly dinoflagellates. In addition, nutrient stoichiometry has changed due to increases in inorganic phosphorus and organic nitrogen and carbon compounds. Furthermore, an unexplained regime shift in phytoplankton biomass occurred between 2000 and 2002, during which time, overall planktonic biomass dramatically increased.