The ballast water and fish farm treatment system for circulating effluent water of a fish farm or a ship by filtering and resupplying the effluent water, the system including a heat exchange system to heat or cool the effluent water, a physical filtration unit to filter out impurities from the effluent water are discharged from the heat exchange system, and a chemical filtration unit to mix the effluent water discharged from the physical filtration unit with chlorine dioxide, wherein the effluent water discharged from the chemical filtration unit is resupplied to the fish farm or the ship. The ballast water and fish farm treatment system allows circulation water of the ship and fish farm to be reused after completely removing parasites, hazardous organisms, germs, and viruses from the circulation water using a combination of physical, chemical and physiological treatment techniques.