Environmental impacts on freshwater ecosystems persist due to inputs of excess fertilizer to agricultural landscapes. Conservation efforts, such as cover crops, are being encouraged to reduce nitrogen (N) and phosphorus (P) runoff from fields, but their effects on working lands are rarely documented. We quantified reductions of nitrate-N and soluble reactive phosphorus (SRP) losses from cropland in response to widespread planting of cover crops in two agricultural watersheds (Indiana, USA) over four water years (2016–2019). We collected water samples bimonthly from tile drains and stream sites to measure nitrate-N and SRP losses across scales.