The St. Johns River (SJR; Jacksonville, FL, USA) is a large, brackish, estuarine system characterized by considerable anthropogenic pollution, recurrent harmful algal blooms (HABs), and diverse toxin-producing cyanobacteria. The most prevalent toxins in SJR water samples are microcystins/nodularins (MCs/NODs). Additionally, the SJR provides critical habitat for a genetically and behaviorally distinct estuarine community of bottlenose dolphins (Tursiops truncatus) that routinely uses and strands in low mesohaline and oligohaline areas of the river. This population has been subject to two unusual mortality events (UME) since 2010 and has since been described as having substantial declines in population health, characterized by widespread dermatitis and emaciation. Additionally, three dolphins have been recovered from low salinity habitats with epidermal algal mats. Because dolphin illness and strandings overlapped temporally and spatially with confirmed cyanobacterial blooms in the SJR, there is concern that estuarine dolphin health may be declining due to exposure to toxic cyanobacteria and HAB events. Specific to this study, the SJR estuarine community was considered a high-risk group for cyanotoxin exposure in relation to coastal animals. This study analyzed all available hepatic tissues for estuarine dolphins, and used samples from coastal individuals that stranded outside of the known cyanotoxin bloom season as controls. Three analytical methods were used to determine MCs/NODs presence in dolphin liver and epidermal algal mat samples. An Adda ELISA and LC-MS/MS were used to determine free MCs/NODs presence while the MMPB technique was used to determine total (bound and free) concentrations and as confirmatory analyses. ELISA analyses produced high values that were not supported by concurrent LC-MS/MS or MMPB analyses, indicative of false positives. MMPB testing resulted in low-level total MCs/NODs detection in some specimens. Results indicate that both estuarine and coastal dolphins are exposed to MCs/NODs, with potential toxic and immune health impacts.