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 (0–210 cm), and N balance sheet on a Huangmian soil (calcaric cambisols, FAO) near Tianshui, Gansu, China. The two main plot treatments were without and with farmyard swine manure (M); sub-plot treatments were control (Ck), N, NP, and NPK.␣The average seed yield decreased in the order MNPK ≥ MNP > MN ≥ NPK ≥ NP > M > N > Ck. The average effect of manure and fertilizers on seed yield was in the order M > N > P > K. The seed yield increase was 20.5% for M, 17.8% for N, 14.2% for P, and 2.9 % for K treatment. Seed yield response to fertilizers was much greater for N and P than for K, and it was much greater for no manure than for manure treatment. The response of straw yield to fertilization treatments was usually similar to that of seed yield. The N fertilizer and manure significantly increased protein concentration and N uptake plant. From the standpoint of increasing crop yield and seed quality, MNPK was the best fertilization strategy. Annual applications of N fertilizer and manure for 23 successive years had a marked effect on NO3-N accumulation in the 0–210 cm soil profile. Accumulation of NO3-N in the deeper soil layers with application of N fertilizer and manure is regarded as a potential danger, because of pollution of the soil environment and of groundwater. Application of N fertilizer in combination with P and/or K fertilizers reduced residual soil NO3-N significantly compared with N fertilizer alone in both no manure and manure plots. The findings suggest that integrated and 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.