Microcystin-LR (MC-LR) was readily biodegraded on addition to six different water samples irrespective of their previous exposure to microcystins. Subsequent studies with water from three of these water bodies confirmed the degradation of MC-LR and also demonstrated the biodegradation of MC-LF, nodularin and mixture of microcystins and nodularin. Rates of degradation of MC-LR, MC-LF and NOD in individual water samples ranged from a half-life of 4 to 18d. Analysis by HPLC-PDA-ESI+ and MALDI MS/MS revealed novel intermediate degradation products of MC-LF and nodularin which included demethylation, hydrolysis, decarboxylation and condensation of the parent compound(s). Our study suggests a possible diversity of micro-organisms and/or pathways which has not been previously observed.