An important way to comprehensively consolidate foundation of food security is risk management of agricultural water resources. The reproduction of ecological service function of water, the economic reproduction of irrigation water, and the reproduction of health of residents involved in agricultural water resources are interrelated under the goal of food security. The risk of agricultural water resources will show the systematic characteristics of cascade amplification if management of agricultural water resources cannot effectively play a buffering role. In practice, agricultural water risk management has achieved positive results, but local risk management thinking cannot effectively prevent and solve agricultural water risks, the difficulties of governance it are as follows: First, rebound effect caused by upgrading of food consumption has expanded the ecological risk of agricultural water resources. Second, the interests of small farmers are not fully protected, resulting in delayed comprehensive reform of agricultural water pricing. Third, groundwater pollution is still serious and difficult to prevent. Fourth, the systemic risk of agricultural water resources is spawned by over-reliance on agricultural water use efficiency improvement. Therefore, we propose to flexibly adjust the objectives and tools of agricultural water resources management with risk-coupled thinking, strengthen economic incentives to control the rebound effect of irrigation water, establish a diversified formation mechanism of agricultural water pricing, and promote groundwater pollution control projects.