Rice-crayfish rotation system is expanding rapidly and becomes the most widely applied crayfish culture modes in the Jianghan Plain, China. However, the wastewater of these operations is directly discharged into the surrounding water system, and the environmental pollution caused by the crayfish culture in the paddy fields is normally neglected and has not been included in the regulatory system of aquaculture regulations. In order to explore the impact of non-point source pollution emission from the rice-crayfish rotation mode on water environment and evaluate rationally its environmental sustainability, the concentrations of total nitrogen, total phosphorus, chemical oxygen demand and ammonia nitrogen in the drainage from the paddy fields after the harvest of crayfish in the Jianghan Plain were monitored. The results showed that the ranges of concentrations of total nitrogen, total phosphorus, chemical oxygen demand and ammonia nitrogen in the effluent were 0.53-5.36, 0.12-0.70, 6.60-78.39 and 0.34-1.75 mg/L, respectively, and the average concentrations of total nitrogen, total phosphorus and chemical oxygen demand all have exceeded the class III water quality standard in the environmental quality standards for surface water (GB 3838-2002). According to the equivalent standard analysis, total nitrogen was the primary pollutant to the environment which showed the highest equivalent standard load ratio. The amounts of discharge of total nitrogen, total phosphorus, chemical oxygen demand and ammonia nitrogen per ton crayfish were 2.994, 0.458, 35.132 and 1.405 kg/t, respectively. The emergy analysis with the integration of environmental pollution showed that the renewable fraction and emergy sustainability index of rice-crayfish rotation system was higher than the rice monoculture system and environmental loading ratio was lower. The results indicated that the non-point source pollution discharge rates of rice-crayfish system were relatively low and rice-crayfish rotation system was more sustainable, as indicated by lower environmental pressure and higher emergy sustainability index. Nevertheless, it is urgent to incorporate wastewater discharged from rice-crayfish farming into the supervision system of aquaculture wastewater discharge regulations and formulate environmental pollution risk control policies to ensure the sustainable development of the rice-crayfish integrated system. The results provided basic data for the further accounting of the pollution contributions of rice-crayfish farming and basis for the non-point source pollution prevention and control, and the sustainable development of rice-crayfish rotation farming.