Water tank experiments were conducted to evaluate the effects of compound bio-nutrient (CB) combination of various nutrient ratios on water environment. In this study, group CK was the blank control group, group A, B and C were CB combinations of organic nutrients, inorganic salts and micronutrients, with the proportion of 16∶78∶6, 32∶62∶6 and 48∶44∶6, respectively. Results showed that dissolved oxygen (DO) concentration in group C had a significant decline, harmful substances content was the highest in group A, in which ammonia nitrogen (NH3–N) level was significantly higher than that in group CK and group B, but there was no significantly difference between group C, and its nitrite (NO2–N) content was increased remarkably compared with other groups. CB gave a great increase to the content of total nitrogen (TN) and total phosphorus (TP), especially in group A and B. A sharp increase of Bacillus counts and a significant decline of Beromonas counts were recorded in all groups treated with CB. In addition, there were an obvious improvement in the abundance and diversity of plankton in all treatments, especially in group B. The results from RDA analysis revealed that TN and TP were the major environmental factor affecting prokaryotes communities, while DO and NH3–N taken effect to eukaryotes communities. In general, the 32∶62∶6 combination of CB in organic nutrients, inorganic salts and micronutrients had good effects on water environmental improvement.