The present study was conducted to evaluate the efficacy of a pollution isolation device in improving water quality in facility-based soft-shelled turtle (Pelodiscus sinensis) aquaculture. A total of 72 soft-shelled turtles, each weighing approximately 300 g, were utilized in this experiment. Two groups were established: one with a small turtle culture pond equipped with a pollution isolation device (treatment group) and another without the device (control group). Water quality parameters, including ammonia nitrogen, turbidity, chemical oxygen demand (COD), and nitrite nitrogen, were monitored and statistically analyzed. The results indicated that the ammonia nitrogen concentration in the treatment group was significantly higher than that in the control group, reaching a maximum of 108 mg/L. The average change rates for turbidity and COD in the control and treatment groups were 14.2% and 8.4%, and 39.5% and 15.5%, respectively. Over the culture period, the control group discharged 286.59 g of COD, 68.33 g of total phosphorus, and 12.32 g of total nitrogen, whereas the treatment group discharged 92.21 g of COD, 46.01 g of total phosphorus, and 5.07 g of total nitrogen. The study demonstrated that, despite the higher ammonia nitrogen concentration in the treatment group, the pollution isolation device significantly reduced the average change rates of turbidity and nitrite nitrogen and decreased the discharge of COD, total phosphorus, and total nitrogen during the culture cycle. Moreover, extending the water exchange period to 15 days effectively reduced the volume of water exchanged and the emission of pollutants. These findings suggest that the pollution isolation device is effective in isolating pollutants and significantly improves water quality in soft-shelled turtle aquaculture systems.