Cyanobacterial blooms and the associated release of cyanotoxins pose problems for many conventional water treatment plants due to their limited removal by typical unit operations. In this study, a conventional water treatment process consisting of coagulation, flocculation, sedimentation, filtration, and sludge dewatering was assessed in lab-scale experiments to measure the removal of microcystin-LR and Microcystis aeruginosa cells using liquid chromatography with mass spectrometer (LC-MS) and a hemacytometer, respectively. The overall goal was to determine the effect of recycling cyanotoxin-laden dewatered sludge supernatant on treated water quality. The lab-scale experimental system was able to maintain the effluent water quality below relevant the United States Environmental Protection Agency (US EPA) and World Health Organisation (WHO) standards for every parameter analyzed at influent concentrations of M. aeruginosa above 106 cells/mL. However, substantial increases of 0.171 NTU (Nephelometric Turbidity Unit), 7 × 104 cells/L, and 0.26 µg/L in turbidity, cyanobacteria cell counts, and microcystin-LR concentration were observed at the time of dewatered supernatant injection. Microcystin-LR concentrations of 1.55 µg/L and 0.25 µg/L were still observed in the dewatering process over 24 and 48 h, respectively, after the initial addition of M.aeruginosa cells, suggesting the possibility that a single cyanobacterial bloom may affect the filtered water quality long after the bloom has dissipated when sludge supernatant recycling is practiced.