With the saline aquaculture pond with ecological engineering farming system as the research object, the drainage channels and reservoirs in the system were used to collect the leaching and infiltrating saline and alkaline water respectively to monitor the saline and alkaline water, nitrogen and phosphorus nutrients in the soil in the system and to conduct comprehensive analysis.  The results show that the total nitrogen and phosphorus in soil and in saline and alkaline water respectively decreased and increased significantly through salt leaching and dealkalization of the soil by infiltrating and leaching. The effect of soil leaching on the elution of ammonia nitrogen, nitrate nitrogen and orthophosphate was weak, but the effect of soil infiltration on elution of ammonia nitrogen was strong. The water in the reservoir used as saline and alkaline water collection tank after soil infiltration has high concentration of ammonia nitrogen and can be used as supplementary water for aquaculture;  the total nitrogen and total phosphorus in aquaculture water of saline aquaculture pond with ecological engineering farming system are < 4 mg/L and < 1.3 mg/L respectively, meeting the requirements of aquaculture.