To evaluate the effects of filter-feeding fishes on water quality and bacterial community in the rice–crayfish coculture system, four different stocking densities of bighead carp (0, 500, 1000, 1500 ind./200 m2) were set up in rice–crayfish coculture systems. Water samples in the systems were collected biweekly to detect dissolved oxygen (DO), temperature (T), potential of Hydrogen (pH), ammonia nitrogen (NH4+-N), nitrite nitrogen (NO2−-N), nitrate nitrogen (NO3−-N), total nitrogen (TN), total phosphorus (TP), and Chlorophyll-a (Chl-a); the bacterial community in the water was analyzed simultaneously, then the correlation between water quality and microorganisms were studied. The results showed that concentrations of TN, TP, NO2−-N, and NH4+-N decreased while DO and NO3−-N increased along with the breeding process. NO2−-N, NO3−-N, TN, and NH4+-N were important environmental factors affecting the bacterial community structure in water (p < 0.05). Bighead carp stocking had an impact on the diversity, richness, and evenness of the bacterial communities in the systems. The dominant bacteria in the four different carp density groups were Proteobacteria, Actinomycetes, Bacteroidetes, and Cyanobacteria. Bighead carp increased the abundance of Bacteroidea but reduced that of Actinomycetes, Cyanobacteria, and Proteobacteria. The introduction of bighead carp promoted the conversion of nitrogen and phosphorus, reducing the risk of cyanobacterial blooms. Group 1000 ind./200 m2 exhibited the best effect on the removal of nitrogen and phosphorus from the water body.