Aquatic macroinvertebrates were collected from five sites in the Neversink Reservoir Watershed in Sullivan County, New York: Aden Brook, Biscuit Brook, Main Branch, Tison and Winnisook, and examined for gill abnormalities. The Neversink Reservoir is part of the New York City water supply system and is located in the Catskill Mountains. Total mercury and methylmercury concentrations were measured by the New York State Department of Environmental Conservation (NYSDEC) in composite samples of macroinvertebrates at the five sites and ranged from 13.6 to 20.9 ng/g total mercury and 2.4–9.8 ng/g methylmercury. Gill deformities in the organisms were evident from each sampling site. These were observed as puckering or dimpling of the gill lamellae and interior spotting. The greatest percentage of gill morphological abnormalities were from invertebrates at the Main Branch site where 28% of invertebrate gills exhibited abnormalities. This site had the highest mercury/methylmercury concentration in composite invertebrate samples. Macroinvertebrates from a reference location showed little evidence of gill abnormalities. Other factors may have contributed to the abnormalities such as dissolved oxygen, pH, temperature, other contaminants, and/or stream profiles.