Properly designed biological filters or infiltration systems have the capacity to significantly reduce effluent concentrations of pathogenic microorganisms in wastewater. The retention and elimination of microbial cells in biological wastewater filter systems is influenced by several factors. In this review, these factors are discussed. Immobilization of microbial cells moving through a porous media is influenced by mechanisms such as physical straining as well as adsorption to porous media. The grain size of porous media and bacterial cell size are important factors affecting the straining of bacteria, as are the hydraulic loading rate or the extent of clogging layer development in the filter. Adsorption of cells to the porous media is influenced by the content of organic matter, degree of biofilm development, and electrostatic attraction due to ion strength of the solution or electrostatic charges of cell- and particle surfaces. The rate of inactivation of pathogenic microorganisms, in adsorbed or liquid phases, has been shown to be affected by abiotic and biotic factors such as moisture content, pH, temperature, organic matter, bacterial species, predation, and antagonistic symbiosis between microorganisms in the system.