Research was conducted to characterize the benthos of the lower Mill River as it empties into the Quinnipiac River and New Haven harbor. The watershed contribution to the health of this watercourse was descrived, along with local threats and future issues concerning the ecological health of the river. Eighteen sites in this one mile reach were studied, supplemented with two nearby sites in the Quinnipiac River for comparison. Sediment concentrations of trace metals, sediment texture, and total carbon and nitrogen content of the sediments were analyzed. The benthic infauna macroinvertebrate community was tabulated. Sediment cores were taken to study accretion and deposition rates.