The fish ecology of Deepor Beel is being threatened by the continuous flow of effluents from the solid wastes of Municipal garbage dump. The present study has been aimed to investigate the genotoxic effect of the solid wastes on Channa punctata of Deepor Beel using micronucleus assay. Fishes were collected from garbage dump affected and unaffected area of Deepor Beel. The micronuclei assay demonstrated significantly higher frequency of micronuclei and other nuclear abnormalities in Channa punctata collected from affected site as compared to unaffected reference site. This study depicted the usefulness of micronucleus assay as an adequate approach for ecotoxicological monitoring of aquatic environment and its biodiversity.