Nutrient-driven cyanobacteria blooms are an increasingly common issue in freshwater environments, particularly in anthropogenically altered landscapes. As stormwater runoff is one of the largest sources of nutrients for freshwater bodies, stormwater retention ponds in urban and suburban areas are likely environments for harmful cyanobacteria blooms and were thus targeted for an in-depth investigation assessing taxonomic composition, bloom morphological composition, toxicity, and impact of nutrients and other environmental drivers. Eighty-seven algal blooms were sampled from 2019 to 2022 in the greater Wilmington, North Carolina, area. Physicochemical parameters were recorded, and blooms were classified by type (defined as surface mat, surface scum, water column distribution, or benthic mat) and dominant taxa. Blooms of potentially toxic cyanobacteria genera in the water column of stormwater retention ponds were most prevalent. Dissolved inorganic phosphorus was significantly related to chlorophyll-α, Microcystis bloom formation, and the production of microcystin. Seventeen potentially toxic cyanobacteria genera were identified in retention ponds, some of whose blooms demonstrated detectable microcystin. Monoclonal cultures isolated from some blooms were found to produce anabaenopeptin and saxitoxin. The results demonstrate a higher incidence of potentially toxic cyanobacteria over other bloom-forming taxa (chlorophytes, euglenoids, chrysophytes, dinoflagellates, and diatoms) in the 39 water bodies sampled. The frequency of blooms occurring in stormwater ponds and the diversity of potentially toxic cyanobacteria identified suggest such harmful blooms are likely widespread in similar freshwater environments across multiple urbanizing areas. The blooms sampled in this study were all within residential, commercial, or recreational areas easily accessible to people, presenting serious hazards to both environmental and public health.