The U.S. Geological Survey (USGS) assessed streams throughout the State of South Dakota during 2008-09 as part of the U.S. Environmental Protection Agency’s (USEPA) National Rivers and Streams Assessment (NRSA) program. NRSA is a probability-based survey of our Nation’s rivers and streams intended to provide a comprehensive “State of the Flowing Waters” assessment. The USEPA established a set of core ecological indicators to be measured at each target site when conditions allowed. These indicators included physical habitat, in-stream characteristics, aquatic vertebrates, periphyton assemblages, benthic macroinvertebrate assemblages, field properties, and water chemistry. During 2008, the USGS-South Dakota Water Science Center conducted stream assessments at 25 of the 61 statewide target sites. A repeat assessment designed to meet established quality-assurance/quality-control requirements was conducted at one of these target sites, designated as a revisit site. During 2009, the USGS completed another 36 stream assessments at target sites, with repeat assessments conducted at three revisit sites. Additionally, three sites characterized as reference sites were visited, bringing the total of visited sites to 64 with 68 physical assessments.

The USGS also was involved in the 2000-04 Environmental Monitoring and Assessment Program-West (EMAP-West). The EMAP-West study’s purpose was to develop the monitoring tools and protocols that would be used in following assessment programs. The 2008-09 program illuminated protocols that were changed from the earlier program. The following were substantial protocol changes: fish sampling was conducted using only electro-shocking techniques, utilizing only one netter (seine nets were not used); fish were vouchered (identified and sent to an EPA-designated laboratory) at only approximately 10 percent of wadeable streams, and fish tissue samples were collected at all boatable sites (during EMAP-West fish were vouchered at each stream); a second, separate composite of benthic macroinvertebrates was collected at low-gradient streams to include information from the edge habitats (during EMAP-West only one composite was collected); and fecal indicators, chlorophyll-a, and periphyton samples were filtered in the field (rather than sent to a laboratory).