Cyanobacteria populate most water environments, and their ability to effectively exploit light and nutrients provide them with a competitive advantage over other life forms. In particular conditions, cyanobacteria may experience considerable growth and give rise to the so-called harmful algal blooms (HABs). HABs are often characterized by the production of cyanotoxins, which cause adverse effects to both aquatic organisms and humans and even threaten drinking water supplies. The concentration of cyanotoxins in surface waters results from the budget between production by cyanobacteria and transformation, including photodegradation under sunlight exposure. Climate change will likely provide favorable conditions for HABs, which are expected to increase in frequency over both space and time. Moreover, climate change could modify the ability of some surface waters to induce phototransformation reactions. Photochemical modeling is here carried out for two cyanotoxins of known photoreaction kinetics (microcystin-LR and cylindrospermopsin), which follow different phototransformation pathways and for particular freshwater scenarios (summertime stratification in lakes, water browning, and evaporative water concentration). On this basis, it is possible to quantitatively predict that the expected changes in water-column conditions under a changing climate would enhance photodegradation of those cyanotoxins that are significantly transformed by reaction with the triplet states of chromophoric dissolved organic matter (3CDOM*). This is known to be the case for microcystin-LR, for which faster photodegradation in some environments would at least partially offset enhanced occurrence. Unfortunately, very few data are currently available for the role of 3CDOM* in the degradation of other cyanotoxins, which is a major knowledge gap in understanding the link between cyanotoxin photodegradation and changing climate.