Gradients of dissolved oxygen concentrations in seasonally stratified estuarine water columns directly influence microbial composition and metabolic pathways, resulting in annually recurring spatiotemporal chemical gradients of redox-active species. Understanding such microbial responses to variable geochemical conditions and elucidating the diversity of microbial processes are needed to comprehensively identify ecosystem functions. At first this study describes an investigation of the relationships between microbial processes and geochemical conditions. To assess the contribution of different biological redox processes on carbon and nitrogen cycles in the Chesapeake Bay, we used observational and experimental approaches as well as utilization of monitoring datasets to facilitate an assessment of ecosystem-level metabolism. Observations revealed a general positive association of community metabolism with strong gradients of redox-related variables and hydrodynamic characteristics, although geochemical and environmental conditions varied seasonally across oxic transitions and interannually across degrees of stratification. The most distinct evidence supporting the positive association were vertical distributions of community respiration with the highest average rates in the most stratified regions coincident with the depths of the steepest gradient of chemical compounds. Although organic matter availability may be enhanced due to hydrodynamically induced stability, our investigation of factors driving the pattern revealed that differential responses and metabolic strategies of microbial communities result in high respiration near oxyclines. Investigation of vertical profiles of redox-related variables also revealed that the coexistence of oxidants and reduced compounds further provides an optimal condition for other electron accepting processes, including chemoautotrophy and anoxygenic photoautotrophy. The strong interdependence between environmental conditions and variability in microbial metabolism also reflected in patterns of plankton assemblages. An ammonium mass-balance analysis revealed that increases in vertical ammonium dispersion during severe hypoxia cause a shift of plankton assemblages towards heterotrophy, subsequently supporting a deep secondary microbial food web in the vicinity of oxic/anoxic interface. Overall, results from this research indicate that the estimation of more accurate net ecosystem metabolism should take into consideration of the highly variable nature of community metabolism associated with both geochemical gradients and stratification.