The main source of water resources in China is agricultural irrigation. With the increase of agricultural scale operation and agricultural mechanization, agricultural irrigation and water resources protection have become one of the main causes of current water environment pollution problems. Traditional water pollution source management methods have serious problems of resource waste and inefficiency. The main purpose of this paper is to integrate microscopic technology images and clustering algorithms to conduct research on the construction of water pollution source management resources. In this paper, we use microscopy technology and clustering algorithm to fuse high-resolution images with GIS data to classify water classes, land and rivers in the images into classes and construct a comprehensive remediation resource construction plan for polluted rivers. The results show that the water pollution source management resource construction scheme based on microscopic technology image and clustering algorithm can significantly improve the efficiency of water resources monitoring; at the same time, it can realize the use of higher resolution land water quality monitoring resources; realize the low investment and operation cost of water pollution source management.