Chlorella lewinii LC172265 and Scenedesmus dimorphus NIES-93 were grown with BG-11 medium and then transferred to fish seedlings' farm and the effects on changes in the pH, nitrite, total ammonia nitrogen and toxic ammonia were studied. Inoculation of the ponds with C. lewinii, S. dimorphus and the combined culture of C. lewinii and S. dimorphus significantly reduced the rise in the pH of the ponds (p<0.05). With these three cultures, the pond pH increased from 6.3±0.03 to only 6.5±0.2, 6.7±0.6 and 6.4±0.1 respectively within a period of 240 hours, as against control pond's pH which increased from 6.3±0.03 to 9.0±0.1 within the same period. Furthermore, inoculation with S. dimorphus reduced the nitrite concentration in the ponds to zero on the 144th hour and the concentration remained zero throughout the experiment. This was closely followed by the combined culture of C. lewinii and S. dimorphus which reduced the nitrite concentration to zero at 240th hour while C. lewinii was the least in nitrite removal. Toxic ammonia was also zeroed by the combined culture of C. lewinii and S. dimorphus at 144th hour of experiment which was followed by C. lewinii (at 192nd hour). Aquaculture ponds co-cultured with microalgae witnessed a maximum fry death rate of 40% which was much lower than 80% death rate observed in the control ponds. These results show that C. lewinii and S. dimorphus are very efficient in sustaining the quality of aquaculture water, and thus prolonging the length of time water can be used before changing.Keywords: nitrogen removal, ammonia, nitrite, fishery, fish pond