Maintaining optimal water parameters in a biofloc technology system is essential for ensuring the healthy growth, development, and survival of cultured aquatic organisms. Fluctuations in these parameters can negatively impact their health, growth performance, and overall survival rate. This study compares the effects of two biofloc-producing bacteria, Bacillus cereus and Klebsiella pneumoniae, on water quality. The study was conducted under sterile laboratory conditions using water with 10 ppt salinity, and water quality parameters were assessed at 24-h intervals. Both bacterial strains were capable of forming bioflocs, though their performance varied over time. Bacillus cereus showed fluctuations in pH (6.5–8.9), whereas Klebsiella pneumoniae maintained relative stability (6–7.4). Both treatments elevated total alkalinity, but K. pneumoniae caused a sharp increase from 150 ppm to 310 ppm, differing from previous observations. B. cereus maintained stable total hardness and dissolved oxygen (2–5 mg/L) but caused elevated turbidity (819 NTU) after floc disintegration. Overall, bioflocs produced by B. cereus were more consistent and exhibited properties better suited for sustainable aquaculture under controlled conditions compared to those formed by K. pneumoniae.