The invention provides a water treatment system for aquaculture. The system comprises a floating platform, an aquaculture water tank, a circulating water pump, a filtering and separating device, fans,a water tank bottom purging system and a biochemical filtering pool, wherein the biochemical filtering pool is connected with the filtering and separating device through a pipeline; the aquaculture water tank is embedded in the floating platform; the circulating water pump comprises a deepwater submersible pump and a surface water submersible pump; the filtering and separating device comprises amicrofiltration machine and a protein separator, the microfiltration machine is connected with the deepwater submersible pump through a pipeline, the protein separator is connected with the surface water submersible pump through a pipeline, and the fans are connected with the water tank bottom purging system in the aquaculture water tank, the protein separator and the biochemical filtering pool through pipelines respectively. According to the water treatment system for aquaculture, aquaculture water and pond water are separated, the aquaculture system is subjected to life support treatment with circulating water, the aquaculture water is purified and flows into a pond for secondary purification, then the water is circulated in the aquaculture water tank, so that water resource is recycled,the purification effect is ideal, and dynamic balance of water is realized.