Water pollution is severe in Ningxia irrigation zone and water quality is classified as Inferior Category V in many of drainage ditches. The main pollutants are nitrate and ammonium. A 5-year swine manure application trial and nitrate leaching losses have been conducted. There are 3 treatments:traditional without manure (CK), traditional matched manure 4500 kg/hm²(T1) and traditional matched manure 9000 kg/hm² (T2). Nitrate nitrogen leaching losses at 30, 60, 90cm soil layers have been measured by resin core method. The results indicate that swine manure application cannot obviously increase soil nitrate leaching losses at 30cm layer. Contrasting with CK (15.96±0.41) kg/hm², T1 (16.85±0.40) kg/hm² and T2 (17.01±0.46) kg/hm² do not reach significant differences (P<0.05), the same result as at the 60cm layer. However there are significant differences between treatments and CK and no significant differences between T1 and T2 at 90cm layer. Manure application can increase soil organic matter and total nitrogen. SOM of T1 and T2 are increased 0.95 and 1.41g/kg, which are improved 7.50% and 11.13%. TN of T1 and T2 are increased 0.06 and 0.16 g/kg at 0~30cm layer, which are improved 7.72% and 22.04%. Manure application can increase crop yield, rice yield is increased 12.26%~11.55%, but also winter wheat yield is increased 9.32%~12.52%.