Leachate and storm-driven runoff from silage storage bunkers can degrade receiving water bodies if left untreated. This study evaluated a novel treatment system consisting of three treatment tanks with a moving-bed biofilm reactor and paired side-by-side denitrifying woodchip bioreactors for the ability to reduce influent nutrient mass loads. Flow-based samples were taken at four locations throughout the system, at the inflow to the first tank, outflow from the tanks prior to entering the woodchip bioreactors, and from the outflows of both bioreactors. Samples were analyzed for concentrations of nitrogen (N) and phosphorus (P) species. Inflow concentrations were reduced from the bioreactor outflows by an average of 35% for total N (TN) and 16% for total P (TP) concentrations on a storm event basis. The treatment system cumulatively removed 76% of the TN mass load, 71% of the nitrite + nitrate-N (NO2−+NO3−-N) load, 26% of the TP mass load, and 19% of the soluble reactive P load, but was a source of ammonium-N, based on the monitoring of 16 storm events throughout 2019. While the system was effective, very low NO2−+NO3−-N concentrations in the silage bunker runoff entered the bioreactors, which may have inhibited denitrification performance.