The treatment of nitrate and phosphate ions in fresh water such as streams, rivers, lakes, reservoirs, and wetlands through biological treatment has been getting more crucial and popular in recent years. This paper reports the reduction of nitrate and phosphate ions in modified low salinity fresh water via the cultivation of a microalgae strain, e.g., Tetraspora sp. and Spirogyra sp. The low salinity fresh water (9054 to 9992 ppm) was modified with the addition of organic fertiliser (VermiCompost Tea) and used as the cultivation medium to grow microalgae. The microalgae strains were grown under controlled conditions in an indoor laboratory for 14 days. The initial concentrations of nitrate and phosphate ions in the modified fresh water sample were 1.17 mg/L and 0.10 mg/L, respectively. The reduction of nitrate and phosphate ions associated with the effect of cultivation of Tetraspora sp. and Spirogyra sp. in ambient air (0.03% of CO2) and 15% of CO2 was investigated. In ambient air, the cultivation of Tetraspora sp. and Spirogyra sp. greatly reduced the nitrate ions concentration from 5.96 ± 0.28 to 0.37 ± 0.05 mg/L and from 2.35 ± 0.19 to 0.59 ± 0.08 mg/L, respectively. A 100% reduction of phosphate ions was observed in the cultivation of Tetraspora sp. and Spirogyra sp. from 0.52 ± 0.10 mg/L in 13 days of and from 0.63 ± 0.15 mg/L in 6 days, respectively. Meanwhile, with the aeration of 15% of CO2, after the 14 days cultivation of Tetraspora sp. and Spirogyra sp. reduced the nitrate ions concentration from 5.27 ± 0.06 to 1.80 ± 0.20 mg/L and from 4.73 ± 0.12 to 2.80 ± 0.10 mg/L, respectively. The excessive CO2 in water consequently lowered the pH of water medium from 7.18 to 6.60 due to the formation of carbonic acid (H2CO3). It was feasible to couple the removal of nitrogen and phosphorus in Sungai Sura (4°42″28.2° N 103°26″12.1° E) while cultivating microalgae through biological treatment to produce biomass for biofuel production.