The global increase in detection of cyanobacteria and their metabolites has prompted greater emphasis in optimizing water treatment options for their effective removal. In particular, conventional coagulation and clarification processes have been shown to be effective in removing whole cyanobacterial cells, and consequently a majority of the metabolites. However, the resultant cyanobacterial-laden sludge is often not closely monitored in treatment plants. This study has shown that the sludge supernatant derived from the coagulation/sedimentation of a range of natural cyanobacterial blooms contained extremely high concentrations of metabolites (up to ∼8,000 ng L–1 of geosmin and ∼90 μg L–1 of microcystins), which was attributed to cell lysis. Furthermore, the fate of the metabolites in the sludge supernatants differed with geosmin shown to be biodegradable, while the microcystins were released at different stages with some variants shown to be more persistent. The release and biodegradation of the metabolites followed pseudo-first-order kinetics with rate constants comparable to experiments using laboratory-cultured cyanobacteria. A key finding from this study was that the identification of cyanobacterial cell type is critical in making informed operational decisions, as not only did the cells behave differently within the sludge, but also the released metabolites behaved quite differently within the time frames studied.