The U.S. Geological Survey and the Wisconsin Department of Natural Resources began a comprehensive, multidisciplinary evaluation-monitoring program in 1989 to assess the effectiveness of the Wisconsin Nonpoint Source Program. Hydrologic, water-quality, habitat, and fish data were collected at Otter Creek from 1990 to 2002 with the pre-BMP (best-management practice) period ending in September 1993 and the post-BMP period beginning in October 1999. BMPs installed in this basin included streambank protection and fencing, stream crossings, grade stabilization, buffer strips, various barnyard-runoff controls, nutrient management, and a low degree of upland BMPs. Reductions between pre- and post-BMP periods were detected in median concentrations of base-flow samples for total suspended solids and BOD5 but not for total phosphorus or dissolved ammonia nitrogen; fecal coliform concentrations in base-flow samples increased over the study period.

Reductions in rainfall storm loads between the pre- and post-BMP periods during the non-vegetative season (November through May) were detected for all three constituents monitored (total suspended solids, total phosphorus, and dissolved ammonia nitrogen). Differences in rainfall storm loads of these three constituents for the vegetative season (June through October) were not detected. When considering rainfall data from the entire year, reductions in storm loads were detected for total suspended solids and dissolved ammonia nitrogen (reductions were estimated at 58 percent for total suspended solids and 41 percent for dissolved ammonia nitrogen). Annual reductions in rainfall storm loads for the non-vegetative season were estimated at 58 percent for total suspended solids, 48 percent for total phosphorus, and 41 percent for dissolved ammonia nitrogen.

Habitat and fish data were collected each year of the study to track the effects of BMPs on stream habitat and fish communities. Final trend analysis was performed using habitat quality index scores, an index of biotic integrity, and some of the originally measured fish and habitat variables. Habitat was improved for stream segments that had either natural riparian buffer or where streambank fencing was installed, but not at the station where the riparian area was pasture and no streambank fencing was installed. The results also suggest that BMP implementation in Otter Creek substantially modified fish community structure, but the overall community quality was not improved.