Water resources development and utilization (WRDU) is an important way for humans to utilize natural resources, and has a deep effect on ecological environments. Flat topography, groundwater dependence and a high proportion of agricultural water are the main features of WRDU in Sanjiang Plain. Due to large-scale development in the last 60 years, the ecological environment of Sanjiang Plain has changed significantly. In order to identify the eco-environmental problems and make regional ecological environment and water resources sustainable, trend and correlation analyses were performed to analyze the eco-environmental effects of WRDU from the aspects of water resources, land resources, vegetation and climate. The results show that the regional eco-environmental effects caused by WRDU in Sanjiang Plain are significant. The quantity and quality of groundwater resources and the social and ecological functions of land resources are significantly affected by the regional development and utilization of water resources, while the effect of surface water resources is not obvious. The changes of vegetation and climate are also significant, but the response mechanism to WRDU requires further study. With the changes of extent, pattern and degree of surface water utilization in Sanjiang Plain, the effect of surface water resources is becoming more and more prominent.