Total nitrogen input and loss from cattle manure, fertilizer, legume crops, precipitation, and domestic septic systems in the upper Snake River Basin, Idaho and western Wyoming, were estimated by county for water year 1990. The purpose of these estimations was to rank input of nitrogen by source, determine the amount of total nitrogen potentially available to both ground and surface water through leaching and runoff, and identify areas in the basin where excess nitrogen is produced. The results of the input estimations suggest that domestic septic systems account for less than 1 percent of the total nitrogen input in the basin and precipitation accounts for 6 percent. The remaining 93 percent is produced by cattle manure (29 percent), fertilizer (45 percent), and legume crops (19 percent). Input from cattle manure, fertilizer, and legume crops varies widely among counties and reflects differences in land-use practices such as different cropping patterns and numbers of dairies and feedlots. Residual total nitrogen was estimated by subtracting loss due to cattle manure storage and application, crop uptake, and decomposition of previous-year nonleguminous crop residue (chaff) from all nitrogen input in the basin. Positive mean values of residual total nitrogen in most counties suggest that more total nitrogen is input than is lost. This residual total nitrogen is available for runoff to surface water or leaching to ground water. Three out of four counties where mean values of residual total nitrogen were highest (Cassia, Gooding, and Twin Falls) are located in the western part of the basin, where eutrophication in the Snake River is evident and ground water from many wells contains anomalously high nitrate concentrations. Ground water in the fourth county (Bingham), which includes the Fort Hall area north of Pocatello, also contains high nitrate concentrations. A mass balance of total nitrogen input and loss in Gooding, Jerome, Lincoln, and Twin Falls Counties suggests that more than 6,000,000 kg (6,600 tons) of total nitrogen is input in this four-county area than is discharged by the Snake River. This excess nitrogen probably is utilized by aquatic vegetation in the Snake River (causing eutrophication), stored as nitrogen in soil, stored as nitrate in the ground water and eventually discharged through the springs, utilized by noncrop vegetation, and lost through denitrification.