The present invention relates to an apparatus for magnetising water for the aquaculture system, comprising of: a culture tank for rearing aquatic organism connecting to an inflow water passage; a filtering tank for filtering effluents having an elongated tubular member connecting to the base of the culture tank for draining water into the filtering tank and a layer of filtering means including a sponge, coral rubbers and gravels with a volume ratio and a centrifugal pump for recirculating filtered water from the filtering tank into the inflow water passage, wherein said filtered water is mixed with fresh water in the water passage; characterised in that a magnetic means having a pair of magnetic plates parallel to the inflow water passage,wherein the magnetic fields generate from said plates magnetise the water flow through the water passage and said filtered water and fresh water will be magnetised to improve the physicochemical properties of the water compound.