The influence of nutrient loading and other anthropogenic stressors is thought to be greater in low inflow, microtidal estuaries, where there is limited water exchange. This 11-month study compared spatial changes in macrofaunal communities adjacent to regions that varied in land cover in Oso Bay, Texas, an estuarine secondary bay with inflow dominated by hypersaline discharge, in addition to discharge from multiple municipal wastewater treatment plants. Macrofauna communities changed in composition with distance away from a wastewater treatment plant in Oso Bay, with the western region of the bay containing different communities than the head and the inlet of the bay. Ostracods were numerically dominant close to the wastewater discharge point. Macrobenthic community composition is most highly correlated with silicate concentrations in the water column. Silicate is negatively correlated with salinity and dissolved oxygen, and positively correlated with nutrients within the bay. Results are relevant for environmental management purposes by demonstrating that point-source discharges can still have ecological effects in hydrologically altered estuaries.