Thau lagoon is a Mediterranean shellfish ecosystem with large biomasses of oysters growing in waters with high residence time due to low tidal ranges, The influence of filter feeders (oysters and their epibiota) on the spatial distribution of particulate and dissolved compounds in the water column of Thau lagoon was studied through its variation with time, In 1991/1992, daily variations were investigated in pens, corridors and outside shellfish farming zones for nutrients, chlorophyll a and primary production. Salinity, dissolved oxygen, nutrients, organic matter and chlorophyll a were also monitored in surface waters inside and outside shellfish farming zones each week from January 1993 to March 1994. The presence of shellfish farms led to a decrease by only a few percent of oxygen concentrations in their vicinity, but the mean (+/- SE) deficits of chlorophyll a and POC concentrations were 44 +/- 4 % and 26 +/- 9 % respectively in the eastern zone (8 m). The shift induced by filter feeders in phytoplankton composition favoured picophytoplankton with higher growth rates. But the summer increase in phytoplankton growth rate was stronger than the positive feedback due to filter feeder filtration. Summer was determinant for the growth of oysters owing to enhanced regenerated primary production. During this period, filter feeders were not food limited, while they tended to control phytoplankton biomasses and production the rest of the year. The nutrient excess in shellfish farming zones was highly significant, with increases of 73 +/- 16, 36 +/- 12 and 19 +/- 8 % for ammonia, phosphates and silicate respectively in the eastern zone. In the western zone, the nutrient excess was less strong by half for ammonia and phosphate, because the lower depth (4 m) allows light to reach the bottom and enables benthic macroflora to grow on nutrients of benthic origin. The decline of phytoplankton biomasses in shellfish farms induced a decrease in the nutrient demand, especially for ammonia. This situation was likely to favour nitrification, which led during autumn to higher nitrate concentrations within shellfish farming zones than outside. Therefore, filter feeders were able to alter the dominant biogeochemical process in the water column by stimulating nitrification.