A water-quality investigation of the upper Snake River Basin began in 1991 as part of the U.S. Geological Survey's National Water- Quality Assessment Program. As part of the investigation, intensive monitoring was conducted during water years 1993 through 1995 to assess surface-water quality in the basin. Sampling and analysis focused on nutrients, suspended sediments, and pesticides because of nationwide interest in these constituents.

Concentrations of nutrients and suspended sediment in water samples from 19 sites in the upper Snake River Basin, including nine on the main stem, were assessed. In general, concentrations of nutrients and suspended sediment were smaller in water from the 11 sites upstream from American Falls Reservoir than in water from the 8 sites downstream from the reservoir where effects from land-use activities are most pronounced. Median concentrations of dissolved nitrite plus nitrate as nitrogen at the 19 sites ranged from less than 0.05 to 1.60 milligrams per liter; total phosphorus as phosphorus, less than 0.01 to 0.11 milligrams per liter; and suspended sediment, 4 to 72 milligrams per liter. Concentrations of nutrients and suspended sediment in the main stem of the Snake River, in general, increased downstream. The largest concentrations in the main stem were in the middle reach of the Snake River between Milner Dam and the outlet of the upper Snake River Basin at King Hill.

Significant differences (p<0.05) in nutrient and suspended sediment concentrations were noted among groups of sites categorized by the quantity of agricultural land in their upstream drainage basins. Water samples collected from sites in drainage basins where agricultural land constituted less than 10 percent of the land use contained significantly smaller concentrations of nutrients and suspended sediment than samples from sites in drainage basins where agricultural land constituted more than 10 percent of the land use. Significant differences in nutrient and suspended sediment concentrations were inconsistent among groups representing 10 to 19 percent, 20 to 29 percent, and greater than 29 percent agricultural land use. Seasonal concentrations of dissolved nitrite plus nitrate, total phosphorus, and suspended sediment were significantly different among most of the agricultural land-use groups. Concentrations of dissolved nitrite plus nitrate were largest during the nonirrigation season, October through March. Concentrations of total phosphorus and suspended sediment, in general, were largest during high streamflow, April through June.

Nutrient and suspended sediment inputs to the middle Snake reach were from a variety of sources. During water year 1995, springs were the primary source of water and total nitrogen to the river and accounted for 66 and 60 percent of the total input, respectively. Isotope and water-table information indicated that the springs derived most of their nitrogen from agricultural activities along the margins of the Snake River. Aquacultural effluent was a major source of ammonia (82 percent), organic nitrogen (30 percent), and total phosphorus (35 percent). Tributary streams were a major source of organic nitrogen (28 percent) and suspended sediment (58 percent). In proportion to its discharge (less than 1 percent), the Twin Falls sewage-treatment plant was a major source of total phosphorus (13 percent). A comparison of discharge and loading in water year 1995 with estimates of instream transport showed a good correlation (relative difference of less than 15 percent) for discharge, total organic nitrogen, dissolved nitrite plus nitrate, total nitrogen, and total phosphorus. Estimates of dissolved ammonia and suspended sediment loads correlated poorly with instream transport; relative differences were about 79 and 61 percent, respectively.

The pesticides EPTC, atrazine, desethylatrazine, metolachlor, and alachlor were the most commonly detected in the upper Snake River Basin and accounted for about 75 percent of all pesticide detections. All pesticides detected were at concentrations less than 1 microgram per liter and below water-quality criteria established by the U.S. Environmental Protection Agency. In samples collected from two small agriculturally dominated tributary basins, the largest number and concentrations of pesticides were detected in May and June following early growing season applications. At one of the sites, the pesticide atrazine and its metabolite desethylatrazine were detected throughout the year.

On the basis of 37 samples collected basinwide in May and June 1994, total annual subbasin applications and instantaneous instream fluxes of EPTC and atrazine showed logarithmic relations with coefficients of determination (R2 values) of 0.55 and 0.62, respectively. At the time of sampling, the median daily flux of EPTC was about 0.0001 percent of the annual quantity applied, whereas the median daily flux of atrazine was between 0.001 and 0.01 percent.