Aquaculture is a rapidly expanding industry in Australia and around the world. The majority of aquaculture operations employ flow through systems whereby residual feed and metabolic products are discharged to a nearby water body. In many countries, the discharge of nutrients rich aquaculture waters has contributed to the degradation of water quality in receiving water bodies. Aquaculture's dependency on water resources ultimately makes water recycling an attractive waste management option. Submerged flow biofilters, utilising a filter media with specific surface area of approximately 141 m3/m3, were used to remove nitrogen and phosphorus from a synthetic fish farm water. Three biofilter systems were tested for nitrification, nitrification followed by denitrification, and combined nutrients removal. Successful carbon removal and nitrification were achieved in the nitrification system. The nitrification/denitrification biofilters achieved complete denitrification and nitrogen removal. The cyclic aerated/unaerated combined nutrients removal system achieved approximately 40 percent phosphorus removal, complete nitrification and 40 percent denitrification. The study demonstrated the viability of using biofilters for nutrients removal from fish farm waters. Biofilters are readily designed and constructed in modular form which makes such systems particularly useful for water quality management in aquaculture.