The upper Blackfoot River in southeastern Idaho receives runoff from 12 large phosphate mines. Waste shales that are removed to access the phosphate ore are highly enriched with selenium, resulting in elevated selenium in runoff from the mine waste dumps. In 2001, in cooperation with the Bureau of Land Management, the U.S. Geological Survey (USGS) began monitoring streamflow, selenium, and other water-quality parameters at a single location near the outlet of the upper Blackfoot River to the Blackfoot Reservoir. Water samples primarily were collected by a flow triggered, automated pump sampler, supplemented by manual point and equal-width integrated manual samples.

The approach to monitoring concentrations and streamflow over time at a fixed location is ideal for evaluating temporal trends, but provides no information about the relative source contributions from the mine waste dumps draining into various tributaries. In 2001, the Idaho Department of Environmental Quality (IDEQ) began an annual, mid-May, synoptic survey of selenium concentrations and streamflow at 21 locations along the main stem Blackfoot River and its tributaries. Individually, neither the intensive USGS sampling at the outlet nor the IDEQ annual synoptic sampling provides a comprehensive view of selenium runoff in the Blackfoot River watershed. Together, the efforts are complementary; therefore, in this report, results are presented from both sampling efforts.

The USGS collected time-series data from 2001 to 2012 at a fixed location, the Blackfoot River near the outlet of the reservoir, near Henry, Idaho (USGS streamgage 13063000). Dissolved selenium concentrations from 450 filtered samples collected at this site ranged from 0.5 to 11.4 micrograms per liter (μg/L). The State of Idaho chronic aquatic life criterion concentration of 5 μg/L was exceeded in 31 percent of the samples, with most exceedances occurring during May of each year. No exceedances of the selenium criterion were recorded in months other than April, May, or June. Concentrations of selenium in unfiltered and filtered samples were similar, and concentrations from samples collected by depth and width integrated methods were similar to those collected by grab (point) samples, indicating that the grab samples adequately represent selenium concentrations across the entire river cross section. In speciation analyses made during 2003 and 2004, the median percentage of total selenium as selenate was 81 percent, ranging from 17 to 98 percent, and the median percentage of total selenium as selenite was 19 percent, ranging from 2 to 83 percent of the total selenium. During the period of study, selenium concentrations had an upward trend during the lowflow season of August–October. Time trends were not obvious during other seasons. Selenium daily loads varied by more than a factor of 900 during the study period and ranged from 0.03 kilograms per day (kg/d) to more than 24 kg/d. Annual maximum daily loads of selenium varied over nearly a factor of 12, ranging from about 2 to 24 kg/d.

For the annual spring synoptic samples collected by the IDEQ along the main stem Blackfoot River and major tributaries, selenium concentrations ranged from less than 2 to 870 μg/L in 176 samples. In most years, the synoptic sampling showed that the majority of the selenium loads passing the USGS streamgage at the outlet of the watershed could be attributed to a single tributary, East Mill Creek, which enters the Blackfoot River through Spring Creek. Selenium loads decreased by about half from East Mill Creek before reaching the Blackfoot River, suggesting that much selenium is at least temporarily removed from the water column by uptake by aquatic vegetation or by losses to sediment. Similar decreases in selenium loads occurred through the main stem Blackfoot River before reaching the outlet in low flow years, but not in high flow years.