Application of chemical fertilizers and farmyard manure affects crop productivity and improves nutrient cycling within soil-plant systems, but the magnitude varies with soil-climatic conditions. A long-term (1982-2004) field experiment was conducted to investigate the effects of nitrogen (N), phosphorus (P), and potassium (K) fertilizers and farmyard swine manure (M) on seed and straw yield, protein concentration, and N uptake in the seed and straw of 19-year winter wheat (Triticum aestivum L.) and four-year oilseed (three-year canola, Brassica napus L. in 1987, 2000 and 2003; one-year flax, Linum usitatisimum L. in 1991), accumulation of nitrate-N (NO3-N) in the soil profile (0-210cm), and N balance sheet on balanced application of N, P, and K fertilizers and manure at proper rates is important for protecting soil and groundwater from potential NO3-N pollution and for maintaining high crop productivity in the rainfed region of Northwestern China.