This study is aimed at testing a new method to improve fishpond water quality in the acid sulfate soil areas by using biogas slurry (BS). Two experiments were implemented on-site at the fishpond to test for quantity of biogas slurry applied and fish growing status. In the first experiment, treatment of 75% BS had water pH increased from 3.3 to 6.5 after 1.5 months; DO values and Chlorophyll-a concentrations were reasonably high (5.2 ppm and 143.05 μg/L). In the second experiment, the daily weight gain of Snakeskin gourami (0.002 g/day) in treatment 1 was significantly lower than that in treatment 2 (0.051 g/day) and treatment 3 (0.049 g/day); however, the survival rate and the fish yield of fingerling nursing in treatment 2 (22.19% and 270 kg/1000 m2) were similar to those in treatment 3 (22.44% and 264 kg/1000 m2). For Climbing perch, the daily weight gain of the fingerlings in treatment I (0.004 g/day) was significantly lower than those in treatment II (0.045 g/day) and in treatment III (0.048 g/day). In conclusion, treatment 75% BS (153 m3/1000 m2) is considered the best rate to improve water pH and produce good yield of fish for farmer’s income.