Lake Lesser Prespa in Greece is a vital breeding habitat for the Dalmatian and Great White Pelican and a shelter for numerous rare and endemic species. However, eutrophication processes are distressing the lake system and the outbreaks of cyanobacterial blooms during the warm months may pose a threat to aquatic organisms due to the presence of microcystins (MCs). In this study we hypothesize that nutrients (eutrophication), nutrient-rich pelican droppings (guanotrophication) and warming (climate change) can affect the algal growth and MCs production in the water layer of Lake Lesser Prespa. Seston collected from three lake sites was incubated at ambient (20°C) and high (30°C) temperature with or without the addition of nutrients (nitrogen (N), phosphorus (P)), or pelican droppings. Results showed increased chlorophyll-a at higher temperature (30°C). N addition yielded higher chlorophyll-a levels than the non-treated water or when only P was added. The addition of both N and P as well as the addition of pelican dropping resulted in the highest chlorophyll-a at both temperatures. Notably, in the dropping-treatments, cyanobacteria and MCs were promoted while changes were evoked in the relative contribution of toxic MC-variants. Guanotrophication may thus influence the cyanobacterial dynamics and most likely their toxicity profile at Lesser Prespa.