The Macau storage reservoir (MSR) has experienced algal blooms in recent years, with high levels of Cylindrospermopsis and Microcystis and detectable concentrations of cyanotoxins. To analyze the cyanotoxin-producing genotypes and relate the corresponding cyanotoxins to the water quality parameters, a quantitative real-time polymerase chain reaction was developed and applied to the water samples in three locations of MSR. Cylindrospermopsin polyketide synthetase (pks) gene and a series of microcystin synthetase (mcy) genes were used for identifying and quantifying cylindrospermopsin- and microcystin-producing genes, and the corresponding water parameters were measured accordingly. Our results showed that high concentrations of cylindrospermopsin and low concentrations of microcystin were measured during the study period. There was a strong correlation between the pks gene numbers and cylindrospermopsin concentrations (R2 = 0.95), while weak correlations were obtained between the mcy genes numbers and microcystin concentrations. Furthermore, the pks gene numbers were strongly related to Cylindrospermopsis (R2 = 0.88), cyanobacterial cell numbers (R2 = 0.96), total algae numbers (R2 = 0.95), and chlorophyll-a concentrations (R2 = 0.83), consistent with the dominant species of Cylindrospermopsis among the cyanobacteria existing in MSR. NH4–N (R2 = 0.68) and pH (R2 = 0.89) were the water quality parameters most highly correlated with the pks gene numbers. These results contribute to monitoring for potential cyanotoxins in raw water.