The release of anabaenopeptins (APs) into source freshwater from cyanobacteria harmful algal blooms (cHABs) has raised concerns due to their reported abundance and inhibitory activity toward carboxypeptidases (CP). This study aimed to determine if chlorination, a widely used drinking water treatment, of AP-A, AP-B, and AP-679 inactivates their ability to inhibit carboxypeptidases A (CPA) and B (CPB). Each chlorinate treated AP's degradation by-products (DBPs) were analyzed via high-resolution mass spectrometry (HRMS) to track structural changes. This analysis suggested that site-specific chlorination begins with tyrosine residues. The resulting DBPs for each AP were then tested with standard enzyme assays to observe inhibitory changes to CPA and CPB. It was observed that AP-B DBPs retained potent inhibition of CPB. The lack of chlorine efficacy in inactivating AP-B is attributed to the ureido group arginine being unaffected by chlorination. As cHABs continue to pose global risks to drinking water supplies, further research is needed on AP inactivation, AP removal by drinking water treatment processes, and the impact of CP inhibition on human health.