Groundwater is one of the important water resources in China. Its advantages include rich reserves, good water quality, convenient access and not easy to lose. According to the groundwater resources survey, two-thirds of cities in China exploit groundwater, which has become the main drinking water source of these cities. Therefore, groundwater is of great significance in protecting the ecological environment and human health. In this paper, Genetic neural network(GNN) algorithm is proposed for regional water environment risk assessment(RA) and ecological health regulation(EHR), and the water environment RA index system based on GNN model is studied and analyzed; The regulation measures of ecological health of water environment are put forward; Taking the groundwater environment of a city as the research object, the regional water environment RA and health regulation test analysis are carried out. The test results verify the effectiveness of the regional water environment RA and EHR based on GNN proposed in this paper, and ensure the rationality of the design of ecological regulation and control scheme, which has strong popularization.