Information on streamflow gains and losses in the lower Boise River Basin is needed by the Idaho Department of Water Resources to determine recharge to and discharge from the ground- water system. A method was developed to select canal and creek reaches such that a minimum of two reaches were measured in each of 12 different areas that share a set of common environmental characteristics. After a large number of environmental characteristics were evaluated, soil type, land use, and canal density were selected to define the 12 areas. Seepage runs were made on 39 irrigation canal and creek reaches in the lower Boise River Basin in June-July and September 1996. During the June-July seepage runs, irrigation canals gained and lost water, whereas in September, most reaches lost. No substantial differences were noted in the median and spread of flow gains and losses within the 12 areas; therefore, no direct relation could be defined between seepage and environmental areas. Seepage runs were made on three reaches of the lower Boise River in November 1996 to identify flow gains and losses after the irrigation season. The two upstream reaches had net gains, whereas the most downstream reach, near the confluence with the Snake River, had a net loss. The total gain to the river from the three reaches was 90.71 cubic feet per second. Because of potential flooding in March 1997, water was diverted from the Boise River into the New York Canal to reduce flows in the river. This allowed a seepage run on the canal when there were no irrigation diversions or return flows. Subsequently, two seepage runs were made in March when flows near Diversion Dam were about 440 and 860 cubic feet per second. Both gains and losses were measured along the canal, but losses were dominant. Total loss from the canal during the first seepage run was -54 cubic feet per second; during the second, -143 cubic feet per second. Sixteen wells near the canal were measured weekly from the last week in February through mid-June. Generally, water levels decreased from February to mid-April and then increased through June. Paired wells near the canal indicated downward movement of water, probably recharge from canal losses. Study results indicate that additional seepage runs are needed on irrigation canals and creeks, the Boise River, and the New York Canal. Piezometers installed at different depths are needed to better define vertical ground-water movement and gradients. Additional work is needed to determine how seepage in canals and streams relates to environmental characteristics.