As groundwater is an important source of drinkable water supplied for human, it concerns human health once chemical pollution occurs. The farmland irrigation and the construction of river conservancy projects all have an adverse impact on groundwater yield and quality. This paper analyzes the hydrogeological conditions of a river, builds a model for surveying chemical contaminants in groundwater. In addition to this, this study also traces the migration and changes of contaminants in underwater. Certain control measures are given against pollution. The findings show that the groundwater in the areas in question has a tendency to increase the concentration of chemical pollutants and deteriorate water quality due to the application of farmland fertilizers; the water quality in most areas has not met the drinking conditions any more.