The biofilm-mediated bioremediation of drinking water source for Microcystin-LR degradation under various water quality parameters was investigated using sand filter with known Microcystin (MC)-degrading bacterial genera: Arthrobacter (A), Bacillus (B) and Sphingomonas (S), both under individual (A, B and S) as well as co-culture condition (A + X, B + X and S + X) with the native bacterial strains (Pseudomonas fragi and Chryseobacterium sp. = X). These native bacterial strains were isolated from the filtration unit of a drinking water treatment plant (DWTP). Before starting the filter operation, the biofilm-forming ability of MC-degraders was evaluated using a unique experimental set-up. The study showed that the MC-LR removal was enhanced by 38% using S + X filter as compared to the uninoculated filter (control). Except for Bacillus sp., MC-degraders in the form of Arthrobacter ramosus and Sphingomonas sp. enhanced the MC removal potential of the native bacterial strains (X) by 10% and 17%, respectively. The central composite design was used to obtain an optimized input parameter (pH, temperature, initial turbidity and retention time) for the filter operation. Various output parameters including dissolved organic carbon (DOC), total coliform, turbidity, dissolved oxygen, MC-LR toxicity and ammonia were analyzed to form a well-generalized model with a desirability index of 0.638. Overall, filter S + X achieved a non-detectable MCs concentration in some cycles and showed an average of >30% DOC and >80% of total coliform removal along with an under-regulated removal of nitrite, nitrate and ammonia. However, MC-LR breakthrough occurred after 8 weeks of filter operation. These studies demonstrated the effectiveness of inoculating MC-degraders in an existing filtration unit of a DWTP to remove the seasonal occurrence of MCs in the water source.