A 3 yr record (1992 to 1994) of dissolved oxygen (DO) concentrations from an intensive grid of 21 sampling stations in a ∼100 km 2 study area of western Massachusetts Bay (∼25 to 50 m water depth) showed a regular seasonal decline in bottom waters during stratification, but considerable spatial and temporal variability within and across years. Mean near-bottom, subpycnocline DO concentrations for the area reached 7.57, 7.85, and 6.2 mg l -1 in mid October 1992, late September 1993, and late September 1994, respectively; individual station readings were as low as 4.8 mg l -1 in 1994. Overall stratified-season rates of subpycnocline DO decline were ∼0.025 to 0.031 mg l -1 d -1 , but rates increased late in the season as the bottom layer sharply warmed to its annual temperature maximum. Concurrent with relatively lower DO concentrations in 1994, field measurements indicated high bottom-water temperatures >12°C (≥4°C above 1992 to 1993) and a deepened pycnocline just prior to overturn. To address how factors like temperature and vertical structure of the water column interact with metabolic processes to shape observed trends in DO decline and spatio-temporal variability, we used a simple model with physical and biological measurements from field monitoring as inputs. From field and model sensitivity results, we conclude that temperature and stratification strongly influence DO minima and rates of decline, and these factors interact with the bathymetric slope, as well as the topographic and depositional heterogeneity of the study area, to create subpycnocline variability in DO. With respect to lower DO in 1994, temperature contributed by accelerating both water and sediment metabolism, but a major effect was the late-season deepening of the pycnocline that enhanced the contribution of sediment respiration to DO decline by isolating a thin near-bottom water layer. In addition, dynamics of seasonal pycnocline deepening are a principal influence on interannual variability in bottom-water DO because, in contrast to the late-season effect, early in the stratified season a shallow pycnocline depth may moderate DO decline by allowing mid-water primary production to add DO to subpycnocline water.