Here, we review the efficient removal of organic micropollutants from water by degradation during filtration using specialized bacteria and enzymes. In both approaches, the filter provides essential binding sites where efficient degradation can occur. A model is presented that enables the simulation and prediction of the kinetics of filtration for a given pollutant concentration, flow rate, and filter dimensions and can facilitate the design of experiments and capacity estimates; it predicts the establishment of a steady state, during which the emerging concentrations of the pollutants remain constant. One method to remove cyanotoxins produced by Microcystis cyanobacteria, which pose a threat at concentrations above 1.0 µg L−1, is to use an activated granular carbon filter with a biofilm; this method resulted in the complete removal of the filtered toxins (5 µg L−1) during a long experiment (225 d). This system was analyzed using a model which predicted complete toxin removal when applied at a 10-fold-higher concentration. Enzymes are also used in filtration processes for the degradation of trace organic contaminants, mostly through the use of membrane bioreactors, where the enzyme is continuously introduced or maintained in the bioreactor, or it is immobilized on the membrane.