The cyanobacterial toxin saxitoxin (STX) is mainly associated with the blooms of marine dinoflagellates, but it is also produced by several species of freshwater cyanobacteria. So far, the degradation of STX has only been demonstrated by physicochemical treatments, but in this study, we demonstrated that natural factors, such as bacterioplankton and sunlight, had the capacity for degrading STX in the eutrophic Lake Arresø, Denmark. Natural lake bacterioplankton could reduce STX concentrations by 41–59%. A similar reduction was shown for four saxitoxin analogs. The exposure of the lake water to natural sunlight or simulated sunlight also reduced both intracellular and extracellular, dissolved STX. During 4–8 h exposure, natural sunlight reduced intracellular STX by 38–52% but increased extracellular, dissolved STX by 7–29%. Corresponding values for simulated sunlight were a reduction in intracellular STX by 16–45% and increased levels of extracellular STX by 10–33%. In particle-free lake water, the two types of sunlight reduced ambient, dissolved STX by 13–17%. The light exposure was observed to damage >94% of the sxtA gene involved in STX synthesis. This study demonstrated that lake water bacterioplankton and sunlight can modify STX by degradation and cell destruction, and that the biosynthesis of STX may be inhibited by exposure to sunlight.