Crop and input prices affect agricultural production and water pollution. Fertilizer prices fluctuated over the past two decades, recently increasing substantially. Corn prices also increased after authorization of the Renewable Fuel Standard. This paper estimates the effect of fertilizer and corn prices on total phosphorus (TP) and dissolved phosphorus (DP) concentrations across 226 Great Lakes region watersheds. Findings indicate that a 10% rise in fertilizer prices reduces TP by 3% and DP by 6.9%. Counterfactual analysis shows that without recent fertilizer price hikes, nutrient concentrations would be higher, underscoring the impact of crop and input prices on phosphorus pollution.