Nitrogen (N) and phosphorus (P) loss from crop production agriculture is transported to adjacent and downstream water bodies, resulting in negative environmental impacts including harmful and nuisance algal blooms. Cover crops are a conservation management practice that replaces bare soil with vegetation outside of the cash crop growing season, purportedly reducing N and P loss by increasing water and nutrient demand in agroecosystems. In this study, we compared nitrate (NO3−-N), total N (TN), dissolved reactive P (DRP), and total P (TP) loads in subsurface (tile) drainage and surface runoff from fields with cover crop management (CC) and fields without cover crop management (NoCC) using continuous monitoring data from 40 agricultural fields located throughout northcentral Ohio, United States (US). We found that average monthly tile NO3−-N and TN loads from CC fields were ~50% less than NoCC fields, while average monthly tile discharge, DRP, and TP loads did not differ between CC and NoCC fields. Cover crops also did not significantly influence average monthly surface metrics. Cover crops reduced monthly totals of tile NO3−-N and TN loads by ~1.0–2.6 kg N ha−1 from January to June (winter and spring), coinciding with critical periods of nutrient loss from agroecosystems in the midwestern US, but increased monthly totals of tile DRP (by 0.4–12.1 g DRP ha−1) and TP (by 1.2–31.6 g TP ha−1) loads during some months. We found similar patterns at the annual time scale whereby CC fields had lesser cumulative annual totals of tile NO3−-N and TN but greater cumulative annual totals of tile DRP and TP. These results show that the influence of cover crops on N loads, but not P, were consistent across temporal scales of examination, demonstrating that cover crops effectively increased N demand and mitigated N losses from agricultural fields. The variable influence of cover crops on P loads underscores the need for greater understanding of the factors and mechanisms that control P loss in systems that include cover crop management. Furthermore, these findings stress the importance of identifying and selecting conservation management practices tailored to the natural resource concern.