This study analyzed concentrations of cyanobacteria and microcystin at a water treatment plant located on the Nakdong River during an algal bloom season. The plant was installed with the pre-ozonation and filter/adsorber process as an advanced process. The sampling, in addition to the raw water, was occurred at the intake well and after each process including pre-ozonation, coagulation and settling, filtration, and disinfection. The results indicated significant reductions in turbidity and chlorophyll-a concentrations as the treatment progressed, demonstrating the effective removal of cyanobacteria. Microcystin was not detected in any of the samples, as cyanobacteria showed overall low concentrations, highlighting the need for further studies during hazardous algal blooms. Additionally, the effectiveness of the intercellular microcystin extraction method was evaluated. Among the extraction methods (i.e., ultrasonic treatment, freeze-thaw, and methanol extraction), the freeze-thaw method proved to be the most effective, while methanol extraction showed relatively lower efficiency. This study underscores importance of water treatment processes in reducing algal cells and their associated toxins and proposes freeze-thawing as the most effective pre-treatment method.