This study focussed on the fate of cyanobacteria cells and associated metabolites during the sludge management processes that follow the conventional drinking water treatment train. The topic is of importance, as the release of metabolites during sludge treatment may pose a risk to water quality if supernatant is recycled to the head of the plant. The study of the kinetics of cell damage and metabolite release into the supernatant is complicated by simultaneous and rapid natural removal processes. In this study, the release of organic material from cyanobacterial sludge was monitored simultaneously with secondary metabolites (microcystins (MCs), cylindrospermopsin (CYN), and geosmin (GSM)) as an additional parameter to aid in understanding the range of processes occurring in sludge. Only GSM produced by Dolichospermum circinale was found to represent a low risk, as the compound is readily degraded. In contrast, the metabolites CYN and MC were shown to increase in concentration during simulated sludge treatment, suggesting that this could occur within full scale sludge treatment facilities with a range of cyanobacteria species, metabolites and water quality. A generic risk matrix was developed, incorporating the type of cyanobacteria, metabolite production, and the treatment processes available to water utilities for the mitigation of the identified risks.