The mesohaline portion of the Chesapeake Bay is subject to annual summertime hypoxia and anoxia in waters beneath the pycnocline. This dissolved oxygen deficit is directly related to salinity-based stratification of the water column in combination with high levels of autochthonously produced organic matter and a very high abundance of metabolically active bacteria. Throughout the water column in the lower, mesohaline part of the bay, between the Potomac and Rappahannock rivers, near the southern limit of the mainstem anoxia, bacterial abundance often exceeded 10 x 10 cells per ml and bacterial production exceeded 7 x 10 cells per liter per day during summer. Bacterial biomass averaged 34% (range, 16 to 126%) of the phytoplankton biomass in summer. These values are equal to or greater than those found farther north in the bay, where the oxygen deficit is more severe. Seasonal variations in bacterial abundance and production were correlated with phytoplankton biomass (lag time, 7 to 14 days), particulate organic carbon and nitrogen, and particulate biochemical oxygen demand in spring; but during summer, they were significantly correlated only with dissolved biochemical oxygen demand. During summer, dissolved biochemical oxygen demand can account for 50 to 60% of the total biochemical oxygen demand throughout the water column and 80% in the bottom waters. There is a clear spring-summer seasonal shift in the production of organic matter and in the coupling of bacteria and autochthonous organic matter. The measurement of dissolved, microbially labile organic matter concentrations is crucial in understanding the trophic dynamics of the lower mesohaline part of the bay. The absolute levels of organic matter in the water column and the bacterial-organic carbon relationships suggest that a lower bay source of organic matter fuels the upper mesohaline bay oxygen deficits.