The base-flow and runoff components of total streamflow at four selected sites in the upper Susquehanna River Basin in New York were calculated through hydrograph-separation techniques from long-term (1941-93) discharge records. Base flow was found to constitute more than 60 percent of the total annual flow of each stream. Base-flow samples were then collected at 18 stream sites several times during 2001 to define the chemical quality of base flow. The concentrations of selected common ions, nutrients, and pesticides were plotted in relation to the amount of agricultural land and carbonate bedrock in the drainage basin upstream of each site. Sites were selected at locations distant from and unaffected by development and urban areas. Twelve of the sites were again sampled in November 2001 for pesticide analysis.

The predominant cations detected in the samples were calcium, magnesium, and sodium; the major anions were chloride, sulfate, and bicarbonate. The predominant nutrient was nitrate. Higher nitrate concentrations in the winter samples than in the summer samples are attributed to the seasonal decrease in plant growth and microbial activity in the streams during the winter, which allows nitrate to persist in the stream water. Lower nitrate concentrations in the summer samples probably result from nitrogen uptake by vegetation and microbial activity in the streams.

Base-flow samples from the agricultural, carbonate-rich northern part of the study area had higher concentrations of most inorganic chemical constituents than those from the forested, noncarbonate (shale, siltstone, and sandstone) central and southern parts. The highest nitrate concentrations were in samples from subbasins dominated by agricultural land, and the lowest were in subbasins dominated by forest. The concentrations in samples from subbasins with forested as well as agricultural land were intermediate.

Six pesticides were detected in samples from 10 of the 12 sites. All were herbicides. The highest concentrations of pesticides, and the most frequent pesticide detections, were in samples from agricultural subbasins and large main-stem subbasins with mixed land use and mixed bedrock geology. A correlation was indicated between land use and concentrations of atrazine and deethylatrazine. The concentrations of all six compounds were at least an order of magnitude lower than New York State and Federal water-quality standards.

Ground water from four production wells in the villages of Afton, Sidney, Unadilla, and Otego was analyzed for chlorofluorocarbons (CFCs) to indicate the approximate age of the water in these wells and the potential for induced infiltration of river water. The water at two of these wells is probably between 26 and 50 years old; the ages of water at the other two wells could not be reliably estimated because of CFC contamination from a nonatmospheric source. The two wells for which CFC analysis gave reliable results (Afton and Otego) probably do not induce infiltration of river water into the aquifer.