The aim of this research is to enhance the bottom environment of Geoje fish farm that has been severely contaminated. Treatment of microbial agent and/or calcium oxide significantly changed that environment: in ignition loss, either treatment (25% or 21%) showed better than mixed treatment (13.2%). In COD, the oxygen releasing agent or mixed treatment reduced the index by more than 20%. In T-P and T-N, the effects of $CaO_2$ on them were overwhelming (50% or more) meanwhile that of the microbial agent on them was less than 20%. Also, $CaO_2$ influenced on the microbial flora: Desulfobvibrio thermophilus, a sulfate reducing bacterium decreased in number, considering the increase of pH and rise of redox potential. In contrast, Pseudomonas sp., Pseudoalteromonas sp., Pseudomonas aeruginosa were remarkably dominant over other species with mixed treatment as a PCA analysis confirmed it.