To determine effects of aquacultured oysters Crassostrea virginica (Gmelin, 1791) on the overlying water column, a mesocosm study was performed at the Marine Ecosystem Research Laboratory (MERL) from June to October, 2000. The MERL facility is located adjacent to Narragansett Bay and consists of fourteen 13,000-l mesocosm tanks designed to simulate the Bay environmental conditions. Two hundred oysters (c35 mm valve height; nominally filtering about 55 l/day/individual) were placed into three mesocosms, and three mesocosms were maintained without oysters as controls. Experiments were run with varying rates of water exchange in the tanks ranging from 0% to 100% per day (13,000 l/day). Parameters that were measured and compared between the two treatments included chlorophyll-a, particulate organic and inorganic matter, sedimentation, nitrate, ammonia, selected phytoplankton species and oyster growth rates. Oysters affected phytoplankton species composition and increased rates of sedimentation. Large diatoms were net sampled, and Nitzchia striata was predominant in mesocosms with oysters, while Skeletonema costatum dominated the control tanks. Ammonia excretion rates were determined for C. virginica using the salicylate–hypochlorite method. Ammonia excretion can be described by the allometric equation E = 50.65w^0.699 when E is the ammonia excretion rate in ug/h, and w is the soft tissue dry weight in grams. Based on rates of ammonia excretion by oysters and observed steady states of ammonia and other forms of inorganic nitrogen in mesocosm tanks, it can be hypothesized that ammonia generated by oysters is taken up by rapidly regenerating phytoplankton in the water column.