Pathogens and the potential risk they present to public health in recreational waters are of continual public concern. The focus of this study was a year-long sampling campaign to document the presence of Microsporidia and protozoan pathogens in the Bayou Texar waterway in Pensacola, Florida. We used biofilms as sentinel indicators for trapping pathogens in five different locations in Pensacola, Florida. Of the 34 biofilm samples, 16 were positive for pathogens. Of these samples, 13 were positive for Enchephalitozoon spp. (mostly E. cuniculi), 11 were positive for Enterocytozoon bieneusi, and two were positive for Cryptosporidium parvum. The data demonstrate that Microsporidia were easily recovered and primarily present in water during summer months.