Rapid industrial expansion and population growth in Indonesia have led to severe water pollution in the Cikakembang River, a tributary of the Citarum River. This study evaluated the potential of microbial bioremediation as a cost-effective and sustainable approach to improve water quality. The experiment evaluated the effects of bacterial type, bacterial ratio, and aeration across twelve treatment combinations. Key water quality parameters such as dissolved oxygen (DO), chemical oxygen demand (COD), ammonia nitrogen (NH3–N), nitrate (NO3−), total nitrogen (TN), and total phosphate (TP) were observed over a 9-day period, with measurements taken every three days. The results showed that bioremediation, particularly when combined with aeration, significantly improved water quality, achieving notable reductions in COD and nitrogen compounds. Significant improvements were achieved under aerated conditions, with average reductions of 82.45% COD, 78.94% NH3–N, 71.83% NO3⁻, 33.49% TN, and 95.62% TP. Combinations B2 and B3, using the first bacterial set and aeration at ratios of 1:50,000 and 1:100,000, showed the highest pollutant removal efficiency. These findings demonstrate the strong potential of microbial bioremediation with aeration for reducing organic and nutrient pollutants in river systems similar to the Cikakembang River.