I wouldn’t call their project bio-filtration, but constructed wetlands. http://water.epa.gov/type/wetlands/upload/design.pdf or http://www.cabmphandbooks.com/Documents/Development/TC-21.pdf It seems like bio-filtration is commonly used to describe bacterial water treatment systems, either aerobic or anaerobic and are usually used in the context of wastewater treatment. Is this what you mean?
Also there is the book ” Constructed Wetlands for Wastewater Treatment and WIldlife Habitat” (case studies) published byt he EPA – this includes the Arcata Wastewater Treatment Marsh, etc. Or the USDA ‘A Handbook of Constructed Wetlands”.
There is another design guideline that we used in school, but I can’t find it right now – essentially had a wetland designed in a series – one forebay for desedimentation, another very shallow heavily planted bay with a ‘creek’ winding through it (this works for desedimentation and nutrient absorption) then a final open bay before discharge into natural systems.
The design depends on what the pollutant is, volume of water, etc.