Microcystin is a naturally occurring liver cyanotoxin that can be found in water bodies around the world. Cyanobacterial blooms occur worldwide and can potentially contaminate municipal drinking water supplies with various toxins. These events are hazardous, naturally occurring processes that can be worsened by anthropogenic activities. The past 50 years have shown notable changes in global climate, likely due to environmentally detrimental human activities. Our environmental impacts have increased the frequency and severity of these events in the past decade. Developments in water quality control and maintenance have greatly reduced exposure to contaminated water, but current methods to detect microcystin are expensive and take several hours to complete. Aptamers are single-stranded DNA sequences with a high affinity to bind to a specific target. A simple to use, aptamer-based method could reduce water quality testing time and cost and allow more frequent testing by quality technicians and consumers alike. Selection of aptamers can be done using an in vitro selection process, Systematic Evolution of Ligand Exchange, combined with capillary electrophoresis.