Microorganisms isolated through artificial media are often unsustainable in biodegrading microcystins (MCs) in natural water. Here we studied alternative approaches to isolate MCs-degrading bacteria using natural media. In comparison to two species (MS-1 and MS-2) isolated from artificial media and the failure of bacterial colonies formation using water extracts of sediment (10%, w/v), five colony species (WC-1 to WC-5) appeared using concentrated water extracts of sediment that is 10-fold enhancement of nutrient level. In the simulated biodegradation test in Lake Taihu water with continuous supply of MCs, a lag phase of 6 days was required for MS-1 and M-2 to degrade 13% and 15% of the added MC-RR and MC-LR, respectively, whereas the lag phase was only 3 days with approximately 44% and 31% removal of the added MC-RR and MC-LR by WC-1 to WC-5. During the continuous supply experiment, degradation of MCs by MS-1 and MS-2 stopped after 3 days, while degradation of MCs by WC-1 to WC-5 lasted continuously throughout the 18 day test period with 2 to 6-fold enhancement of removal rate. 16S rRNA gene sequences and phylogenetic analysis indicated the potential to amplify species of MCsdegrading bacteria when natural media were used. The results suggested that the increased adaptability of bacteria obtained through concentrated natural media was responsible for the enhanced and continued biodegradation under simulated natural water conditions.