Cyanobacterial outgrowths are naturally occurring processes in eutrophic aquatic ecosystems. Furthermore, as a result of climate change and anthropogenic pollution, cyanobacteria harmful algal blooms (CyanoHABs) are expanding worldwide. CyanoHABs are considered a threat to human health and environment due to the production of potent toxic substances, but at the same time, valuable products can be obtained from these microorganisms. The main objective of this study was to test straightforward and cost-effective methods to reduce the toxin content of cyanobacterial biomass for the exploitation of this important biological resource. To carry out this study, lyophilized or hydrated biomass from microcystin-LR (MC-LR) producing Microcystis aeruginosa and cylindrospermopsin (CYN) producing Chrysosporum ovalisporum strains were subjected to the following treatments: (1) thermal (50 °C); (2) ultraviolet (UV) radiation; (3) ozone; and (4) sunlight, for periods varying between 2 and 12 h. MC-LR and CYN concentrations were quantified by LC-MS and compared between experimental groups. The results show a significant reduction in the amount of MC-LR in M. aeruginosa biomass (lyophilized and hydrated) exposed to sunlight. Since no other treatment reduced MC-LR in M. aeruginosa biomass, this molecule was demonstrated to be very stable. Regarding CYN, the concentration of this toxin in C. ovalisporum biomass was significantly reduced with the exposure to UV radiation, to approximately 51% of the initial concentration after 2 h of exposure; 86% reduction after 5 h of exposure; and 77% reduction after 12 h of exposure. Overall, this study demonstrates that the toxicity of cyanobacterial biomass can be reduced by employing environmentally friendly and cost-effective treatments with sunlight and UV radiation.