Biotreatment of aquaculture water for recirculation purposes is a sensible mean to support the further growth of aquaculture industry without excessive water demands that are environmentally unsustainable. This study evaluates the efficacy of biofilter treatment of an eel (Anguilla japonica) culture pond water using different filter media and flow scheme arrangements. The experimental results demonstrate that biofilter systems packed with suitable filter media are capable of improving the quality of effluents for recirculation applications. The characteristics of the filter media appear to be more critical than biofilter flow scheme arrangements in affecting the efficacy of the biofilter treatment. Filter media with surface and structural characteristics are conducive to the development of biofilms and the capture of organic suspended matter are desirable to ensure good and consistent biofilter performance. Under such circumstances the bacterial "consortia" in the biofilter are capable of utilizing the captured organic suspended matter as an alternative substrate to support their metabolic activities when the concentration of the primary substrate (i.e., BOD) is low. For the eel pond water, a biofilter packed with filter media having cross-link structures and a high bed porosity, followed by another biofilter packed with a type of filter media having rough surfaces, produced the best results under the conditions tested. Moreover, a preliminary cost-benefit analysis confirms its cost advantages.