Biological clogging in unsaturated soils is an important concern in the design of biofilters that are used to treat wastewater in rural areas. Several conceptual models have been developed to simulate biological clogging in saturated flow systems but limited research has been performed to develop similar conceptual models in unsaturated soils. This study developed three conceptual models for biological clogging in unsaturated soils. The model formulations varied from microscale to macroscale and from analytically derived to empirical equations. They were all formulated based on the approaches proposed by Burdine and Mualem 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, which incorporates Monod kinetics to simulate the biodegradation of an organic substrate. The three conceptual models that were developed relate the relative permeability to the microbial growth term in the unsaturated flow equation. The models were implemented in a numerical model to illustrate the impact of microbial growth on the biological clogging of unsaturated soils. Also the effect of continuous loading versus pulse loading was simulated to illustrate the difference between the loading scenarios on the clogging process within biofilters.