The Iowa River’s South Fork drains 78,000 ha of glacial terrain. Subsurface drainage is extensive and corn and soybean rotations occupy 85% of the watershed. There are about 100 confined livestock operations in the watershed, most producing swine. Given prevailing practices, we estimate manure from these operations is annually applied to 27% of the watershed, at 200 kg N ha^-1 yr^-1 preceding corn, a rate that may lead to soil P accumulations. An inventory of conservation practices and residue cover was conducted during May 2005. A sequence of USDA-NASS annual crop cover data was used to identify and map crop rotations. We found that 87% of the area in corn in 2004 had adequate (>30%) residue cover at the next planting, whereas, only 47% of the 2004 soybean acreage had >30% residue. This raises concerns for the common practice of fall-applying manure into soybean residue. Decreases in residue and increases in soil P are likely consequences, which can interact to magnify runoff P losses. Stream discharge and nutrient concentrations are being monitored at stream and tile gauges in the watershed. Concentrations of NO₃-N and total P exceed ecological thresholds most of the time (>70%). But the economic value of NO₃-N losses, in terms of fertilizer costs, are about 20 times that of P. Producers therefore have economic incentive to decrease N leaching, but economic incentives to reduce P losses are comparably small. Management alternatives and conservation systems that can reduce losses of both nutrients are needed.