Yes both bacteria and fungi and sometimes coupling of bacteria and fungi used. But it depends on the target compounds you want to remove from water (I guess you are interested in wastewater). Often I see volatile compound removal through fungi biofiler is effective or by coupling of bac-fungi.
In every biofiler the microbiual populatiopn is mixed one. It doesn´t matter of the treated matrix is wastewater or biofilter. It is aldo very important if biofilter is aerobic or anaerobic. The mixed microbial population in an aerobic biofilter treating wastewater contains all microbes listed by Pierlorenzo and protozoa could be present, too.