Cyanobacterial blooms in Thailand waters contain microcystin (MC) hepatotoxins that are a risk to animal and human health. The biodegradation of MCs is a safe and natural method of removal from water. The [Dha7] MC-LR was purified by chromatography, identified by liquid chromatography–tandem mass spectrometry (LC-MS) and used for examining the biodegradation of MCs. Analysis of MC levels revealed degradation of the [Dha7] MC-LR by the bacterium Novosphingobium sp. KKU15, with complete degradation occurring within 3 days under conditions in batches of a flask experiment. The ability of the bacterium to degrade the MCs through a slow sand filter was also investigated. Removal of the [Dha7] MC-LR by biological sand filtration was assessed using a polyvinyl chloride column experiment. In MC-dosed water, degradation of the MC was observed specifically in the inoculated samples (bacterial concentration of 1.6 × 107CFU/cm3 of sand), with complete degradation occurring within 7 days compared to the uninoculated controls. A polymerase chain reaction (PCR) specifically targeting the 16S rRNA gene of Novosphingobium sp. KKU15 was used to monitor the presence of the bacterium in the experimental trials. PCR products indicative of a bacterial population were observed at all of the sample sites in the column where the degradation of the MCs was observed, indicating that this bacterial isolate was active in the degradation of MCs.