Lake Lesser Prespa and its adjacent pond, Vromolimni in Greece, is a shallow freshwater system and a highly protected area hosting an exceptional biodiversity. The occurrence of microcystins (MCs) producing cyanobacterial blooms in these waters during recent years can be harmful to the wildlife. We tested the hypothesis that both cyanobacterial biomass and MCs are strongly influenced by nutrients (eutrophication) and warming (climate change). Lake and pond water was collected from two sites in each water body in 2013 and incubated at three temperatures (20°C, 25°C, 30°C) with or without additional nutrients (nitrogen +N, phosphorus +P and both +N and +P). Based on both biovolume and chlorophyll-a concentrations, cyanobacteria in water from Lesser Prespa were promoted primarily by combined N and P additions and to a lesser extent by N alone. Warming seemed to yield more cyanobacteria biomass in these treatments. In water from Vromolimni, both N alone and N+P additions increased cyanobacteria and a warming effect was hardly discernible. MC concentrations were strongly increased by N and N+P additions in water from all four sites, which also promoted the more toxic variant MC-LR. Hence, both water bodies seem particularly vulnerable to further N-loading enhancing MC related risks.