Oyster aquaculture is a rapidly expanding industry in the Chesapeake Bay. Experiments were conducted to investigate the biogeochemical impact of a commercial oyster aquaculture facility on downstream waters at a facility on Maryland's Eastern Shore. An algal production system (ATS) was installed at the facility to assess the potential for bioremediation and algal production in an integrated multi-trophic aquaculture system (IMTA). Results of the experiments showed an increase in available ammonia downstream of the aquaculture facility, coupled with decreases in dissolved oxygen and total phytoplankton. The algal production system demonstrated an average productivity rate of 82.8 g/m2day-1, a nitrogen (N) removal rate of 9.6 gN/m2day-1, a phosphorus (P) removal rate of 0.20 gP/m2*day-1, and harvests consisted of an average of 7.8% organic content. Productivity and N and P removal rates from this study are higher than other systems tested in the Chesapeake Bay region at sites without an aquaculture facility.