Based on extensive field investigations and a comprehensive analysis of existing literature, we aim to elucidate the distinctive characteristics and identify the primary sources of pollution in small reservoirs across China. Moreover, we examine the factors contributing to the deterioration of water quality and proposes an integrated approach to pollution control and ecosystem restoration, encompassing a framework of “comprehensive pollution control - systematic restoration - integrated management and protection”. To tackle the diverse pollution sources, including fertilizer aquaculture, non-point source runoff, sediment, and water pollution stock, a principle of classified and targeted application is advocated. Furthermore, considering the unique pollution patterns observed in the riparian zones, front dam areas, tributaries, and bay areas, we discuss precise pollution control measures aimed at specific partitions. We also recommend to implement aquatic bioremediation regulations and comprehensive management strategies based upon pollution source interception and load reduction. The findings of this study establish a solid theoretical foundation to maintain the long-term water quality of small reservoirs and support the sustainable water supply management in rural regions.