Nitrogen (N) and phosphorus (P) from agricultural landscapes have been identified as primary sources of excess nutrients in aquatic systems. The main objective of this study was to evaluate the effectiveness of prairie filter strips (PFS) in removing nutrients from cropland runoff in 12 small watersheds in central Iowa. Four treatments with PFS of different spatial coverage and distribution (No-PFS, 10% PFS, 10% PFS with strips, and 20% PFS with strips) were arranged in a balanced incomplete block design across four blocks in 2007. A no-tillage two-year corn (Zea mays L.) –soybean (Glycine max [L.] Merr.) rotation was grown in row-cropped areas beginning in 2007. Runoff was monitored by H flumes, and runoff water samples were collected during the growing seasons to determine concentrations of nitrate-nitrogen (NO₃-N), total nitrogen (TN) and total phosphorus (TP) through 2011. Overall, the presence of PFS reduced mean annual NO₃-N, TN, and TP concentrations by 35%, 73%, and 82%, respectively, and reduced annual NO₃-N, TN, and TP losses by 67%, 84%, and 90%, respectively. However, the amount and distribution of PFS had no significant impact on runoff and nutrient yields. The findings suggest that utilization of PFS at the footslope position of annual row crop systems provides an effective approach to reducing nutrient loss in runoff from small agricultural watersheds.