This study aimed to evaluate the after-effects of cyanobacterial cell removal and lysis by photocatalysis in water. A low concentration of 50 mg/L Ag/AgBr/TiO2 was applied to inactivate Microcystis aeruginosa under visible light irradiation. Most of the M. aeruginosa was killed within 5 h while microcystins-LR (MC-LR) was released into water and accumulated to a high concentration of 100 μg/L. Organic constituents released from cell damage led to 70 mg/L of total organic carbon (TOC) in water. The release of MC-LR and TOC would affect the biostability in the receiving water. Further, mineralization of cell lysis after photocatalysis over a long time resulted in the release of nutrients in water which would be a risk to cause cyanobacterial blooming again. Therefore, these after-effects should not be ignored when photochemical catalysis is applied to mitigate cyanobacterial blooming. Perhaps the best treatment is to remove intact cyanobacterial cells from water and then treat them off-site, for example by anaerobic digestion.