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A field study was initiated in 1992 to investigate the long-term impacts of application of beef feedlot manure (composted and un-composted) on soil nutrient accumulation and movement. Of particular interest were comparisons of two strategies for application to provide annual crop nitrogen requirements (N basis) or to meet crop phosphorus removal (P basis), as well as an inorganic fertilizer treatment. Additionally, effects of a winter cover crop were evaluated. Irrigated corn (Zea mays L.) was produced annually from 1993 through 2002. Average silage yields and crop nutrient removal were highest at the high manure application rates (N basis), intermediate at the low manure application rates (P basis) and least with inorganic N fertilizer. The winter cover crop substantially depleted soil moisture in the spring in some years, resulting in silage yield reductions in 4 of 10 years in the presence of a winter cover treatment. However, the cover crop did significantly reduce NO3-N accumulation at the bottom of the root zone in latter years of the study, most likely due to immobilization of manure N near the soil surface. Soil apparent electrical conductivity (ECa) measured throughout the growing season in 2002 showed significant correlation with surface NO3-N concentration. Higher ECa values during most of the growing season for the no-cover treatments suggest that substantial amounts of manure-mineralized N were being immobilized early in the growing season in the winter cover treatments. The composted manure N-basis treatment (CN) resulted in significantly greater soil profile NO3-N concentrations and higher soil P concentrations at the soil surface. While repeated annual application of beef feedlot manure to supply the total crop N requirement may be acceptable for this soil for several years, sustained application over many years carries the risk of unacceptable accumulation of soil P.