The microbial metabolism for the decomposition of organic matter necessitates the continuous presence of oxygen (Azim et al., 2007). The addition of carbonaceous substrate to the water may result in sudden and temporary lower dissolved oxygen (DO) concentrations. Anecdotal data suggest that such DO drops can result in fish mortality (Colt, 2006). Secondly, excessive turbidity may have negative effects on sensitive fish species and not all are adaptable to growing in turbid water (Avnimelech, 2006). Although preference should be given to basic BFT, i.e., co-culture of aquaculture species and heterotrophic bacterial biomass within the same solution, the considerations mentioned above sometimes require the application of BFT in a compartmental design as was described by Avnimelech (2006). In such applications, the culturing of fish and the microbial production are performed in separate compartments. This allows for a better control of turbidity, oxygenation and return of microbial protein back into the fish compartment.