To ensure the quality of water from Yandong and Yanzidong, which is used to recharge Yilong Lake, meets the required standards, the water quality and pollution sources of Tuanshan-Yandong-Yanzidong section of the Lujiang River in Yilong Lake were investigated and analyzed. Based on the current water pollution status in this river section, an in-situ river management system combining comprehensive interception, absorption, and purification was developed and experimentally validated. The results show that the river section is severely polluted, with total nitrogen (TN) levels significantly exceeding standards, prominent karst pollution, and water quality classified as class IV or lower. The in-situ river management system can significantly improve TN pollution in the river section, the TN contents in the overlying and interstitial water of the simulated river channel show decreasing trends, with the actual average reduction rate for TN in the overlying water rate of 49.99%.