Agricultural land and water use, wastewater treatment facility discharges, land development, road construction, urban runoff, confined-animal feeding operations, reservoir operations, and river channelization affect the water quality and biotic integrity of the lower Boise River between Lucky Peak Dam and the river's mouth at Parma, Idaho. During May 1994 through February 1997, 4 sites on the Boise River, 12 tributary/drain sites, and 3 wastewater treatment facilities were sampled at various intervals during the irrigation (high-flow) and post-irrigation (low-flow) seasons to determine sources, concentrations, and relative loads of nutrients and suspended sediment. Discharge entering the Boise River from the 12 tributary/drain sites and 3 wastewater treatment facilities was measured to determine the nutrient loads being contributed from each source. Total nitrogen, total phosphorus, and suspended sediment concentrations and loads tended to increase in a downstream direction along the Boise River. Among the 15 sources of discharge to the Boise River, 3 southside tributary/drains and the West Boise wastewater treatment facility contributed the largest loads of total nitrogen; the median daily load was more than 2,000 pounds per day. The West Boise wastewater treatment facility contributed the largest median daily load of total phosphorus (810 pounds per day); Dixie Drain contributed the largest median daily load of suspended sediment (26.4 tons per day). Nitrogen-to-phosphorus ratios at the four Boise River sites indicated that phosphorus could be limiting algal growth at the Diversion Dam site, whereas nitrogen could be limiting algal growth at the Glenwood and Middleton sites during some parts of the year. Algal growth in the Boise River near Parma did not appear to be nutrient limited. Because of the complexity of the plumbing system in the lower Boise River (numerous diversions and inflow points), accurate comparisons between discharge and nutrient loads entering the river at measured sites during high-flow sampling periods were difficult. During low-flow sampling periods, southside tributary/drains contributed most of the discharge and total nitrogen load, and wastewater treatment facilities contributed most of the total phosphorus load to the Boise River. During the 50-day period July 18 through September 5, 1996, the Idaho State standard for maximum daily average temperature for coldwater biota was exceeded by 34 percent at Middleton, 48 percent at Caldwell, and 80 percent near Parma. Violations of State standards for primary and secondary contact recreation were observed at all tributary/ drains and in the Boise River near Parma. Median instantaneous concentrations of fecal coliform bacteria exceeded State standards for primary contact recreation at five tributary/drains and exceeded standards for secondary contact recreation at one tributary/drain (Dixie Drain).