This study explores the in vitro effects of cyanotoxins from the methanolic extract of the cyanobacteria Aphanizomenon flos-aquae and Microcystis aeruginosa on human blood cells, with samples drawn from the Gruža reservoir in Serbia. These cyanobacteria, which made up 98.5% of the reservoir’s phytoplankton, reached densities of 4,656,450 cells mL−1, with A. flos aquae (3,105,120 cells mL−1) as the dominant species, followed by M. aeruginosa (1,480,130 cells mL−1). A cyanotoxin analysis of biomass detected anatoxin-a (3.56 µg g−1), cylindrospermopsin (6.86 µg g−1), microcystin LR (0.87 µg g−1), and microcystin RR (2.47 µg g−1). This study assessed the genotoxic potential of the methanolic extract of the cyanobacterial biomass by evaluating the DNA damage and the Genetic Damage Index (GDI) in peripheral blood lymphocytes (PBLs) from healthy donors. The results showed a dose-dependent increase in the DNA damage, from 35.67 ± 4.93% at 10 µg mL−1 to 95.67 ± 1.53% at 100 µg mL−1, with a corresponding rise in the GDI from 0.61 ± 0.02 to 2.39 ± 0.07. The extract also caused the concentration-dependent hemolysis of red blood cells, with 5.63% hemolysis at the highest concentration (200 µg mL−1). These findings underscore the significant genotoxic risks posed by cyanotoxins from biomass extracts of A. flos aquae and M. aeruginosa, particularly in water sources used for human consumption.