The widespread proliferation of potentially toxic cyanobacteria in source waters for drinking water treatment plants (DWTPs) presents a pressing contemporary challenge. Although catalytic wet peroxide oxidation (CWPO) has been recognized as a highly effective and environmentally friendly technology for removing cyanotoxins from water, the simultaneous degradation of cyanobacteria and cyanotoxins has been scarcely investigated. Considering their great morphological diversity, in this work, the impact of the presence of pure strains of several species of toxic and non-toxic cyanobacteria on the degradation of relevant cyanotoxins has been evaluated considering also the main stages of their life cycle. In each studied scenario, achieving a full eradication of the cyanobacteria also led to the complete elimination of the cyanotoxin, including both intra and extracellular fractions. Morphological factors, including filament and cell sizes, play a crucial role in the efficiency of the process. Small cells and long filaments entail a higher presence of particulate organic matter, which consumes hydroxyl radicals considerably in competence with the cyanotoxin degradation. Moreover, the growth stage emerges as a pivotal factor in understanding the CWPO process performance, with cyanobacteria in their early life stages, exhibiting more pronounced interference compared to later stages, probably due to their higher cell viability and accelerated metabolism. All these understandings are essential for the successful implementation of the technology in treating surface waters affected by toxic cyanobacterial blooms.