Long-term monitoring data from agricultural watersheds are needed to determine if efforts to reduce nutrient transport from crop and pasture land have been effective. Goodwater Creek Experimental Watershed (GCEW), located in northeastern Missouri, is a high-runoff-potential watershed dominated by claypan soils. The objectives of this study were to: (i) summarize dissolved NH4-N, NO3-N, and PO4-P flow-weighted concentrations (FWC), daily loads, and yields (unit area loads) in GCEW from 1992 to 2010; (ii) assess time trends and relationships between precipitation, land use, and fertilizer inputs and nutrient transport; and (iii) provide context to the GCEW data by comparisons with other Corn Belt watersheds. Significant declines in annual and quarterly FWCs and yields occurred for all three nutrient species during the study, and the decreases were most evident for NO3-N. Substantial decreases in first-and fourth-quarter NO3-N FWCs and daily loads and modest decreases in first-quarter PO4-P daily loads were observed. Declines in NO3-N and PO4-P transport were attributed to decreased winter wheat (Triticum aestivum L.) and increased corn (Zea mays L.) production that shifted fertilizer application from fall to spring as well as to improved management, such as increased use of incorporation. Regression models and correlation analyses indicated that precipitation, land use, and fertilizer inputs were critical factors controlling transport. Within the Mississippi River Basin, NO3-N yields in GCEW were much lower than in tile-drained areas, but PO4-P yields were among the highest in the basin. Overall, results demonstrated that reductions in fall-applied fertilizer and improved fertilizer management reduced N and P transport in GCEW.