An ecological risk assessment was conducted on the risk to fish of chemical contaminants detected in the habitat of Albula vulpes in South Florida, to evaluate whether contaminants may be a driver of declines in the recreational bonefish fishery. All available contaminant detection data from Biscayne Bay, Florida Bay, and the Florida Keys were compared to federal and state guidelines for aquatic health to identify Contaminants of Potential Ecological Concern (COPECS). For these COPECs, species sensitivity distributions were constructed and compared with recent detections at the 90th centile of exposure. Copper in Biscayne Bay was identified as the highest risk of acute and chronic effects to fish, followed by a risk of chronic effects from both the recently phased-out pesticide endosulfan in Florida Bay, and the pharmaceutical hormone estrone in the Florida Keys.