The increase of toxic cyanobacterial blooms in aquatic ecosystems posing threat to human health has caused countries to establish monitoring strategies and set limit values in their regulations. The frequency of toxic cyanobacterial blooms increase in Turkey as a result of deterioration of water resources. In order to investigate the problems arising from cyanobacteria and cyanotoxins, the 'SIYANOTOKS' Project was carried out by the Ministry of Forestry and Water Affairs, General Directorate of Water Management in cooperation with Istanbul University Faculty of Fisheries. Within this scope, the Project has been carried out to monitor cyanobacteria and their toxins in 18 selected waterbodies: 7 natural lakes, 8 reservoirs, 1 lagoon and 2 coastal and transitional waters in Turkey. Samples were collected between May to October 2015 in monthly intervals and two samples were taken in winter 2015 and Spring 2016. Potentially toxic cyanobacteria species were detected in 14 waterbodies and blooms were observed in 57% of them. A highest concentration of Microcystin-LR eq. was 29.7 mu g/l and cylindrospermopsin was 9 mu g/l. These results showed that cyanotoxin problems are very common in Turkish surface waters and regulation in drinking and recreational waters should be implemented.