Cyanobacteria blooms are common in many of Florida’s most important lakes, rivers and estuaries; threatening water quality, surface drinking water supplies, public health and aquatic ecosystems. In 1998, following the formation of the Florida Harmful Algal Bloom Task Force, a collaborative investigation of cyanotoxins in Florida?s surface waters was initiated by the St. Johns River Water Management District, Florida Marine Research Institute, Florida Department of Health and Wright State University. Project objectives include: (1) identify surface waters that experience extensive cyanobacteria blooms; (2) collect and identify potential toxigenic species; (3) screen samples for the detection and isolation of algal toxins; (4) characterize algal toxins present in water and animal tissues. Approximately 135 water samples have been collected from 125 surface water bodies throughout the state and analyzed for the presence of cyanotoxin(s); including microcystin(s), cylindrospermopsin, anatoxin-a, anatoxin-a(s) and paralytic shellfish poisons (PSPs). Methods used for the detection and characterization of algal toxins include mouse bioassay, enzyme-linked immunosorbent assay (ELISA), protein phosphatase inhibition assay (PPIA), anticholinesterase assay (AA), HPLC-MS/MS and HPLC-Fl. Results indicate that Anabaena sp., Microcystis sp. and Cylindrospermopsis raciborskii are the primary bloom forming cyanobacteria in Florida. The state-wide distribution of C. raciborskii and recent developments of severe blooms (>500 ug/L Chl a) and dominance (relative % biovolume = 97.4) by this species in many of Florida’s lakes has raised concerns for ecological and human health. Surface water samples dominated by C. raciborskii were found to be toxic by mouse bioassay with HPLC results suggesting the presence of a compound similar, but not identical, to cylindrospermopsin identified from Australian waters. Relationships between surface water quality and the production of cyanotoxins, and concerns for present and future drinking water supplies, will be discussed in terms of specific management actions required to reduce the impact of harmful algal blooms in Florida.