Cyanobacterial blooms in drinking water supply affect its quality, which ultimately impacts ecosystem and public health. Thus, this cross-sectional study was conducted to perform a preliminary study on cyanotoxins via analysis of samples collected only once from two sites during the month of peak algal bloom and to subsequently prompt a comprehensive risk assessment in a major drinking water source, Legedadi Reservoir, of Addis Ababa, the capital city of Ethiopia. Samples were collected during peak algal bloom month (January 2018) from two sampling sites, near the dam (S1) and at the center of the reservoir (S2). Identification and enumeration of phytoplankton taxa were done and the measurement of common hepatotoxin (MCs and NOD) concentrations was conducted using liquid chromatography-tandem mass spectrometry. In the reservoir, cyanobacteria made up to 98% of total phytoplankton abundance, with Dolichospermum and Microcystis spp, dominating the phytoplankton community. In these first cyanotoxin analyses conducted for a drinking water supply source in Ethiopia, six major MC variants, namely MC-dmRR, MC-RR, MC-YR, MC-dmLR, MC-LR, and MC-LA, were detected in both algal seston and water samples. MC-LR was the most dominant MCs variant, while nodularin was not detected for both sampling sites. Extracellular total MC concentrations (μg L−1) of 453.89 and 61.63 and intracellular total MC concentrations (μg L−1) of 189.29 and 112.34 were recorded for samples from S1 and S2, respectively. The high concentrations of extracellular MCs, with MC-LR constituting the greatest proportion, indicate the extremely high potential public health risk for end-users.