Cyanobacteria, commonly called blue-green algae, are gram-negative bacteria that play a crucial role in aquatic ecosystems by contributing to oxygen production through photosynthesis and supporting primary productivity, but high population densities of these algae can pose significant ecological and public health risks due to their toxin production. These toxins have been linked to the deaths of dogs and in humans to nervous system damage, liver disease, and skin irritation. Toxigenic strains of cyanobacteria have been identified in Austin’s urban waterways, posing a public health concern for the city. This study examines the presence of cyanobacteria, associated toxins, and water chemistry parameters in Austin’s waterways. Sampling across seven creeks and two creek mouths revealed that six of the nine sites contained cyanoHABs (Cyanobacterial harmful algal blooms, large growths of cyanobacteria that can be harmful to humans and animals), with Oscillatoria as the dominant genus. Liquid chromatography-mass spectrometry (LC-MS) detected cylindrospermopsin as the primary toxin, with concentrations varying across locations. We have detected cylindrospermopsin above the 3 μg/L concentrations that is considered potentially harmful to human and animal health. Physical and chemical water parameters such as temperature, conductivity, nitrate, phosphate, dissolved oxygen, and pH were measured to assess environmental factors influencing algae bloom formation. These findings confirm that cyanobacteria exist in several Austin creeks, indicating the need for ongoing monitoring, particularly in recreational areas.