The onsite disposal of wastewater within the Patchogue River Basin-a riverine estuary that discharges into Great South Bay, Suffolk County, Long Island, N.Y. -has adversely affected water quality and aquatic habitats within both the tidal and non-tidal portions of the river. In response to increased development within the approximately 14 square mile basin, the Village of Patchogue has expanded efforts to manage and protect the local groundwater resources, which sustain freshwater base flow and aquatic habitats. Water-quality samples from 10 shallow wells within the Village were collected in March 2009, before the start of seasonal fertilizer application, to document the effects of onsite wastewater disposal on groundwater discharging into the Patchogue River. Each sample was analyzed for physical properties (pH, dissolved oxygen, specific conductance, and temperature), nutrients, organic carbon, major ions, and trace elements. Water samples from eight wells were analyzed for stable isotopes of nitrogen. The nitrate concentration in one well was 40 milligrams per liter (mg/L), which exceeded the U.S. Environmental Protection Agency (USEPA) and New York State Department of Health (NYSDOH) maximum contamination level in drinking water of 10 mg/L. Sodium concentrations at nine wells exceeded the USEPA Drinking Water Advisory Taste Threshold of 60 mg/L. Dissolved iron concentrations at three wells exceeded the NYSDOH and USEPA Secondary Drinking Water Standard of 300 micrograms per liter (?g/L). Nitrogen isotope signatures (d15N) were determined and compared with those reported from previous studies in Nassau and Suffolk Counties to identify possible sources of the nitrate. Local variations in measured ammonia, nitrate, total nitrogen, phosphorus, and organic carbon concentrations and d15N signatures indicate that nitrate enters the surficial aquifer from several sources (fertilizer, septic waste, and animal waste) and reflects biogeochemical processes such as denitrification.