In recent years, biological floating bed technology has been applied increasingly in aquaculture ponds. In this study we developed a novel floating bed made from ceramsite and studied its effect on water quality, phytoplankton, bacteria and fish growth. Water quality was effectively regulated and controlled in ceramsite floating bed (CFB) ponds with an average transparency of 23.18 cm, ammonia nitrogen (NH4+-N) of 2.30 mg L−1, total nitrogen (TN) of 5.09 mg L−1 and total phosphate (TP) of 1.32 mg L−1 which are lower than in control ponds without CFB. Increased phytoplankton species diversity, bacterial number, metabolic activity and microbial diversity was observed with CFB. At the end of growth stage, feed conversion ratio (FCR) was reduced with a total fish yield of 14,838 kg ha−1 at a survival rate of 77.2% in CFB ponds, which is significantly higher than control (P < 0.05). These results emphasize the potential of ecological floating bed to improve water quality, microalgal diversity, reduce the risk of harmful algal blooms and increase the number, activity and diversity of microorganisms as well as fish yield.