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This study aimed to characterize the bacterial communities in rearing water treated with commercial plastic biological ball filters named as Bio-ball in marron culture for 60 days. Inclusion of Bio-ball in the aquaculture tanks showed improvement in water quality parameters and enrichment of bacterial communities in terms of operational taxonomic units. The water treated with Bio-ball showed significantly less nitrate, nitrite, ammonia, phosphorus and high dissolved oxygen concentration than untreated control group. At phylum level, Proteobacteria was dominant in both control and treated water, whereas Firmicutes was found to be significantly (P < 0·05) enriched in Bio-ball treated water. Among the classified genus, Aquabacterium and Polunucleobacter were most dominant in control and Bio-ball treated water respectively. Linear Discriminant Analysis Effect Size exhibited 31 indicator bacterial genus, 10 in control and 21 in treated condition, suggesting the enrichment of microbial lineages with addition of Bio-ball. The bacteria Haliscomenobacter, Hypnocyclicus, Pajaroellobacter and Vibrio were found to be significantly (P < 0·001) correlated with higher pH, nitrate, nitrite, phosphorus and ammonia in control tanks, whereas Corynebacterium was linked to higher temperature in treated water. Overall results suggest that Bio-ball filter media significantly improved the water quality and microbial populations in aquaculture tanks. SIGNIFICANCE AND IMPACT OF THE STUDY: The results of this study revealed the positive impacts of Bio-ball in enrichment of microbial flora associated with the degradation process of nitrogenous and organic compounds. Bio-ball also showed the capability to prevent the colonization of harmful bacteria, and favoured the growth of beneficial microbes in aquatic system. This study therefore could pave the ways of increasing the aquaculture production by improving the water quality.