As part of federal programs to reduce nutrient pollution, states across the Midwest have developed nutrient reduction strategies, which focus on implementation of agricultural conservation practices (ACPs) or best management practices (BMPs). Despite several decades of federal investment in implementing ACPs/BMPs for reducing nutrient pollution, nutrient pollution is a continuing and growing challenge with profound implications for water quality and public health as well as ecological functions. Pollutant transport depends on water and sediment fluxes, which are governed by local hydrology. Therefore, knowing how flow conditions affect nutrients export is critical to develop effective nutrient reduction strategies. The objective of this study was to investigate the role of streamflow duration curve in controlling nutrient export in the western Lake Erie Basin and the Mississippi River Basin. To achieve this goal, we used long-term monitoring data collected by the National Center for Water Quality Research. We focused on the percentage of the annual pollutant load (nitrate-NO3-N, dissolved reactive phosphorus-DRP, total phosphorus-TP, and total suspended solids-TSS) exported during five flow intervals that spanned the flow duration curve: High Flows (0–10th percentile), Moist Conditions (10–40th percentile), Mid-Range Flows (40–60th percentile), Dry Conditions (60–90th percentile), and Low Flows (90–100th percentile). The results show that the top 10% of flows (i.e., high flows) transported more than 50% of the annual nutrient loads in most of the studying watersheds. Meanwhile, the top 40% of flows transported 54–98% of the annual NO3–N loads, 55–99% of the annual DRP loads, 79–99% of the annual TP loads, and 86–100% of the annual TSS loads across the studying watersheds. The percentage of the annual loads released during high flows increased as the percentage of the agricultural land use in the watershed increased, but it decreased as the watershed area increased across different watersheds. Finally, flow condition/nutrient export relationships were consistent over studying period. Therefore, reducing nutrient loads during high flow condition is the key for effective nutrient reduction.