This paper describes the first use of aerial observations by a drone as an additional means for choosing sampling points during field studies of cyanobacterial harmful algal blooms (CyanoHABs) in selected Bulgarian waterbodies and the use of HPLC analysis of marker pigments for the fast determination of phytoplankton composition and biomass. The selection of waterbodies was based on the authors’ personal expertise and data collected over a 25-year period. In all sites chosen by drone, there were high levels of cyanobacteria and cyanotoxins were present: microcystins (MC-LR, MC-RR, MC-YR in Durankulak Lake and MC-LR and MC-RR in the Sinyata Reka Reservoir), cylindrospermopsin (in the Vaya Lake and in the Mandra Reservoir) and saxitoxins (in Durankulak Lake). The finding of cylindrospermopsin is the first in Bulgaria, the detection of saxitoxins is the first for Durankulak Lake and the microcystins records are the first for Sinyata Reka Reservoir. Considering the high total number of wetlands in Bulgaria, many of which are lowland, small and shallow and therefore vulnerable to CyanoHABs, we recommend further use of drones and HPLC in monitoring, which should speed up detection and reduce sampling efforts while enabling valuable information to be gathered.