In this study, a full survey of pollutant sources and water quality was conducted, followed by the application of a water quality model (Water Quality Analysis Simulation Program, WASP) to establish strategies of water quality control in Carp Lake, Taiwan. Results of the field investigation show that both point and non-point source (NPS) pollutants were responsible for the poor water quality. The contributions of biochemical oxygen demand (BOD) from point source and NPS pollution were 45.9 and 55.1%, respectively. About 80% of total phosphorus (TP) were contributed by NPS. Additionally, point source and NPS pollution discharged 55.5 and 44.5% of NH3–N load, respectively. The Carlson's Trophic State Index ranged from 61.9 to 69.2 showing serious eutrophic problems in Carp Lake. The calculated BOD, NH3–N, and TP carrying capacity were approximately 2.8, 0.42, and 0.15 kg per day, respectively. However, the current pollutant loadings are approximately 3.0–5.5 times the calculated carrying capacity. With the help of the calibrated WASP model, remedial strategies for the lake water from short-term to long-term were developed. The completion of the small local sewer system to remove 80% of the point source pollution can serve as a short-term goal while 40–60% of NPS removal by natural treatment systems may serve as a mid-term goal. Furthermore, 80% of both source point and NPS pollution removal can be considered as a long-term strategy. Results of heavy metal analysis show that the enriched sediment would be safe for agricultural applications.