The scientific and public awareness of hazardous photosynthetic prokaryotes (cyanobacteria/cyanoprokaryotes) and especially the contamination of drinking-water reservoirs with cyanotoxins is world-wide increasing. Recently much more attention has been paid to the events and results of mass proliferation of these toxic organisms even in South-East European countries in spite of the fact that, as a rule, they are not controlled by national legislation. The present paper presents a summary of results of such studies carried out in summer-autumn periods of the last 15 years (2000-2015) in Bulgarian water bodies differing by location, morphometry and trophic status, incl. drinking-water reservoirs, recreational lakes and sites of nature conservation importance. A multivariate analysis allowed to outline the distribution patterns and environmental drivers of the planktonic cyanoprokaryote assemblages in relation with the available data on the water bodies, highlighting species composition and abundance of the main taxa, including potentially toxic species. Samples analysis by HPLC-DAD and/or LC/MS, ELISA and in vitro cytotoxicity tests allowed detection of microcystins, nodularins and saxitoxins. Toxin concentration ranged between 0.1 and 26.5 μg L–1 in water samples and between 10.9 and 1070 μg g–1 (d.w.) in concentrated (net) samples. Despite the fact that microcystins were not found in all studied water bodies and that the recorded levels were still lower in comparison with some other European countries, the fact that cyanotoxins were detected in 16 water bodies (incl. 3 drinking-water reservoirs) could serve as an alert for the need of recognition of cyanotoxins as a new health risk factor in the country. Therefore, permanent monitoring with identification of toxins in water bodies at risk and activities for limitation and control of toxic blooms are urgently needed, in combination with increase of the attention to the effects of cyanotoxins on both human health and health of aquatic ecosystems in Bulgaria.