Grain producers are challenged to maximize crop production while utilizing nutrients efficiently and minimizing negative impacts on water quality. There is a particular concern about nutrient export to the Gulf of Mexico via loss from subsurface drainage systems. The objective of this study was to investigate the effects of crop rotation, tillage, crop residue removal, swine manure applications, and cereal rye (Secale cereale) cover crops on nitrate‐N (NO3‐N) and Total Reactive P (TRP) loss via subsurface drainage. The study was evaluated from 2008 through 2015 using thirty‐six 0.4‐ha plots outfitted with a subsurface drainage water quality monitoring system. Results showed that when swine manure was applied prior to both corn (Zea mays L.) and soybean (Glycine max (L.) Merr.), drainage water had significantly higher eight‐yr‐average flow‐weighted NO3‐N concentrations compared to swine manure applied before corn only in a corn‐soybean (CS) rotation. The lowest NO3‐N loss was 15.2 kg N ha−1 yr−1 from a no‐till CS treatment with rye cover crop and spring application of urea ammonium nitrate (UAN) to corn. The highest NO3‐N loss was 29.5 kg N ha−1 yr−1 from swine manure applied to both corn and soybeans. A rye cover crop reduced NO3‐N loss, whereas tillage and residue management had little impact on NO3‐N loss. Losses of TRP averaged < 32 g P ha−1 yr−1 from all treatments. Corn yield was negatively affected by both no‐till management and cereal rye cover crops. Results showed that cropping management affected N leaching but impacts on P leaching were minimal.