The U.S. Geological Survey in cooperation with the Idaho Department of Water Resources Treasure Valley Comprehensive Aquifer Management Planning effort investigated seasonal groundwater gains and losses on the Boise River, Idaho, starting in November 2009 through August 2010. The investigation was conducted using seepage runs in 11 subreaches over a 14-mile reach from downstream of the inactive streamgage, Boise River below Diversion Dam (U.S. Geological Survey station No. 13203510) to the active Boise River at Glenwood Bridge streamgage (U.S. Geological Survey station No. 13206000). The seepage runs measured mainstem discharge, and significant tributary contributions and diversions along the reach. In addition, an evaluation of the groundwater hydraulic gradient was simultaneously conducted through shallow groundwater mini-piezometers adjacent to the river during February (low stream discharge) and May (high stream discharge) measurement timeframes. November discharge estimates, representative of autumn, had gains and losses that varied by subreach with an overall net gain of 42 ± 8 cubic feet per second (ft³/s). This finding compares favorably to a previous U.S. Geological Survey seepage investigation in November 1996 that found a gaining reach with an estimated gain of 52 ft³/s. This finding also is supported by a U.S. Geological Survey investigation in the study reach in November 1971 that estimated a gain of 74 ft³/s, which largely came from groundwater. The February discharge estimates, representative of winter conditions, showed variability in the reach with a net gain of 52 ft³/s with an uncertainty estimate of ± 7 ft³/s, which is consistent with the low stream discharge findings from November 2009. This finding is further supported by the differential hydraulic head measured at transect sites that qualitatively indicated groundwater to surface-water movement with few exceptions. The May discharge estimates, representative of the spring-time conditions, were gaining or potentially gaining in all but one of the upper subreaches between Boise River below Diversion Dam and Boise River near MK Nature Center sites, with seepage run results supported by hydraulic head differentials indicating a groundwater to surface-water movement. The lower end of the study reach between Boise River near MK Nature Center and Boise River at Glenwood Bridge sites showed more variability with observed hydraulic head differentials that partially supported the potential gains or losses in the reach. Overall, the reach had a calculated net gain of 24 ± 51 ft³/s and, therefore, this estimate may or may not reflect the actual conditions in the reach. The groundwater gains and losses in August, representative of summer conditions, varied in both the upper and lower parts of the reach, with a net loss of -88 ± 69 ft³/s. Overall, the reach experienced a net gain from groundwater at low stream discharges (November and February), a net loss to groundwater at moderately high stream discharge (August), and an ambiguous finding at a higher stream discharge (May). The hydraulic head differentials measured between the groundwater and surface water largely supported the calculated gain and loss estimates in the subreaches, with a potential for groundwater to surface-water movement at low stream discharge in February, and variability during high stream discharge conditions in May.