Agronomists consider the continuity and nutrient capturing properties of cover crops as important determinants of nutrient cycling in agricultural systems. Managing for these biotic control functions can help limit nutrient loss and groundwater contamination between main crop harvests. This simulation study highlights the potential role of cover crop management in a welfare economics framework. The objective is to find the optimal combination of nutrient input to the main crop, the extent of off-season cover crops, and crop functional diversity to maximize the sum of benefits from agricultural production and groundwater protection.