The bay straddles the Florida-Alabama state line.
Officials with the Escambia County Utilities Authority dispute the findings by Robert Livingston. The officials accuse him of trying to deflect attention from International Paper Company, which is paying for his research and owns a mill that is polluting the bay.
The researcher says Bayou Marcus sewage treatment has been overwhelmed by heavy rains over the past 10 months, releasing raw sewage into the bay.
The Florida Department of Environmental Protection also questions Livingston's claims and considers Bayou Marcus to be a model plant.
The facility daily discharges four million gallons of treated effluent into wetlands for more filtering before it empties into the bay.