Possible inexpensive adsorbent sources are urgently required to remove metals and pollutants from aquaculture effluents. Thus, this study evaluated the intensive bacterial production and metal removal (Mn, Co, Ni, Cu, Zn, Pb and Cd) from marine water, which will be used for the culture of aquatic animals using biofloc technology (BFT). In the presence of sugarcane bagasse (T1) and rice-bran (T2) as organic carbon sources, marine polluted water was treated for 6 weeks. As expected, the bacterial numbers increased throughout the experimental period, which helped in breaking down the carbon source and metal removal. Overall, the percentages of heavy metal removal from water samples with different biofloc, and the sequence of adsorption of heavy metals from polluted marine water were Pb > Cu > Ni > Cd > Mn > Co > Zn for T1. Meanwhile, a slight difference was detected in the sequences of T2 as: Pb > Ni > Cu > Cd > Mn > Zn > Co. Furthermore, the relationships among different carbon sources, heavy metals and microbes were also analyzed using the principal component analysis (PCA) and correlation matrix. However, the bacterial and metal profiles have variability by 97.20% at the end of the experiment. The results of this study indicate that the heavy metals concentrations are affected by the bacteria and carbon sources directly via changes in their concentration which provides the opportunity to mitigate the impact of polluted water on the environment so far and provide the opportunity to use water free of heavy metals in aquaculture practices.