The contamination of urban rivers substantially threatens urban ecology, public health, and general progress. Addressing this matter is complex and challenging, particularly in tidal rivers. After investigating the climate conditions, population, and distribution of rivers and pollution in Sanya, China, a hydraulic and water quality model was built for Sanya utilizing InfoWorks ICM, and a comprehensive remediation approach was proposed. The implementation of this scheme led to a substantial decrease in point and non-point sources of pollution. In particular, COD, NH3-N, and TP were reduced by 87.00%, 84.01%, and 74.24%, respectively, from point source pollution. Point source pollution was well-managed north of the bridge, with a reduction rate close to 40% for non-point source pollution. This research confirmed that pollutants are only temporarily retained in the river at high tide and are discharged as the tide recedes, thus having a limited impact on long-term pollution discharge. This research provides valuable references for applying water environment models and the comprehensive treatment of tidal river pollution. The final plan scheme is to significantly improve the water quality of Sanya’s rivers by effectively controlling the discharge of pollutants while achieving considerable cost savings of approximately CNY 1.7 billion.