Frequent records and health concerns in recent times have directed more attention on freshwater cyanobacterial and dinoflagellate blooms in Sri Lanka. Physico-chemical factors influencing phytoplankton growth are still under debate. This necessitates understanding environmental trends governing the dominance and distribution of algal blooms. Hence this study aimed to assess the dominance of Cyanobacteria and Dinoflagellata in reservoirs of Sri Lanka covering the three major climatic regions of the country, the Wet, Intermediate and Dry Zones. Plankton samples were collected using open type 20 µm plankton net and identified using standard phytoplankton keys. Ninety-one species belonging to three phyla of phytoplankton were identified. Phylum Chlorophyta represented the highest species number followed by Bacillariophyta and Cyanophyta. Fourteen genera of Cyanobacteria were recorded and eleven of them were potentially toxigenic. The widest distribution was shown by Chroococcus and Merismopedia. Cylindrospermopsis raciborskii with the highest mean relative abundance was recorded in Intermediate and Dry Zone reservoirs. Peridinium aciculiferum was the only dinoflagellate species recorded during the study with the highest abundance in the Isinbessagala rocky pond. Except sixteen reservoirs which were mesoeutrophic, all the other studied reservoirs were found to be either eutrophic or hypereutrophic. Iranamadu tank recorded the highest TP concentration (236 µg L-1) value. NO3-:TP ratio revealed the phosphate limited conditions in Wet and Dry Zone reservoirs whereas N was a limited factor in Intermediate Zone. Canonical Correspondence Analysis (CCA) results revealed that Secchi depth and area of water spread are important in determining both site and species variations in reservoirs of Sri Lanka.