In this lab-scale research study, the treatment of simulated fish pond water was explored by means of sequencing batch reactors (SBRs) as an external compartment of the bio-flocs technology. This approach was set up with the goals (1) to provide a simple reactor design for application in intensive aquaculture, (2) to determine the effect of the C/N ratio on the assimilation of the ammonia nitrogen in microbial biomass rather than nitrifying it into nitrate and (3) to assess floc quality (protein and poly-bhydroxybutyrate) and floc morphology.