The effect of fish feed quality has gained increasing attention to alleviate the harmful environmental impacts induced by intensive aquaculture. In current research, we have conducted an incubator experiment to highlight the effect of fish feed quality on aquaculture water environment. Fish feed from three manufactures with two different dosages (0.1000 g, 0.2000 g) was added to the culture medium with and without Microcystis aeruginosa. Treatments with Microcystis aeruginosa were named as MHT, MHP and MZT; while the treatments without Microcystis aeruginosa named as HT, HP and ZT. Microcystis aeruginosa densities and nutrients concentrations were measured in the study. Results have shown that fish feed quality (manufactures) has a great effect on nutrients concentrations in the absence of Microcystis aeruginosa (P < 0.05). Meanwhile, fish feed can stimulate Microcystis aeruginosa growth that is also influenced by fish feed quality excluding lag phase (0~12 day) significantly in general (P < 0.05). The maximum Microcystis aeruginosa density (Nmax) is 1221.5, 984.5, 581.0, 2265.9, 2056.8 and 1766.6 1 × 104 cells mL-1 for MHT 0.1 g, MHP 0.1 g, MZT 0.1 g, MHT 0.2 g, MHP 0.2 g and MZT 0.2 g, respectively. In treatments with algae, fish feed quality affect total phosphorus (TP) concentrations (except the difference between MHT and MHP) and total nitrogen (TN) concentrations significantly (P < 0.05). For most of consumed nutrients, the obvious differences among all treatments were observed excluding lag phase in general (P < 0.05), which suggest that the nutrient utilization is also dependent on fish feed quality. Keeping in mind the above facts it is concluded that fish feed quality is a key factor in impacting aquaculture water environment.