Abstract: As part of the environmental impact assessment studies of brackish water aquaculture, the effect of benthic disturbance caused by manual removal of overlying sediment near to the suction sump of an aquaculture pond was studied in the Vellar estuary. The abundance and vertical distribution of meiofauna before and after disturbance were compared. Sediment core and water samples from the pre-and post-disturbance stages were analyzed for meiofaunal abundance, TOC, texture, porosity and physicochemical parameters. Immediately after one day of the benthic disturbance, a drastic decrease in meiofaunal numbers was observed, indicating the deleterious effect of disturbance. On the other hand considerable increase in TOC and meiofaunal numbers from the adjacent sites was observed vouching for the positive impact of such disturbances.