Bunker silos produce a runoff that is a source of nutrient loss and a threat to surface water quality. Little information is available on the water quality of stormwater produced from bunker silos. This research evaluated the runoff characteristics from six horizontal bunker facilities at dairy farms to determine runoff water quality and nutrient loading throughout a storm and annual nutrient losses. On average, at 50% of the cumulative runoff volume the difference between cumulative nutrient load and volume did not exceed 20%, which is a threshold required for a first flush scenario (cumulative loads of P and N were 1.5 to 4.5% and −2.8 to 4.0% greater than cumulative volume, respectively). During the storage of silage in horizontal bunker silos an estimated 0.3 to 1.8% of ensiled P and 0.4 to 1.7% of ensiled N was lost annually with silage runoff. Assessment of a theoretical dairy farm in WI has a calculated runoff loss from horizontal feed storage of 30% and 55% of the total farmstead N and P runoff losses, respectively. Nitrogen (N) and phosphorus (P) loading from bunker silos were relatively consistent throughout a storm with no evidence of a first flush scenario. Annual variability in low flow N and P concentrations were impacted by the production of silage leachate, and bunkers with subsurface collection reduced the nutrient concentrations in overflow runoff. Dairy bunkers provide an opportunity to decrease nutrient loading, through management of a small land base, as compared to other farmstead runoff areas. Reducing the amount of silage runoff lost from dairy farms has strong potential for N and P conservation.