The processes governing clogging of unsaturated soils have a significant impact on the performance of biofilters and septic systems. Several researchers have developed conceptual models for clogging in saturated flow systems. However, limited research has been completed to develop similar models for clogging in unsaturated soils. The objective of this study was to develop conceptual models of the biological clogging process for incorporation into an unsaturated flow and transport code. Three conceptual models were proposed to relate the microbial growth to the relative permeability term in the unsaturated flow equation. The models were formulated based on the approaches used by Burdine (1953) and Mualem (1976) to estimate the relative permeability based on the effective water saturation and the soil moisture curve. A one-dimensional unsaturated flow and transport code was developed. The code includes Monod kinetics to simulate the growth of the microbial mass. Based on published values for the density of the microbial mass, the void space occupied by the microbial mass was determined. The proposed relationships for the relative permeability term in the unsaturated flow equation are a function of the water content (vol/vol) and the microbial mass content (vol/vol). The conceptual models have been developed and implemented in the flow and transport code. Model simulations were performed to illustrate the impact of continuous loading versus pulsed loading on the clogging process within a peat biofilter.