Strongly sorbing chemicals (e.g., heavy metals, radionuclides, pharmaceuticals, and explosives) in porous media are associated predominantly with the solid phase, which is commonly assumed to be stationary. However, recent field- and laboratory-scale observations have shown that in the presence of mobile colloidal particles (e.g., microbes, humic substances, clays, and metal oxides), colloids can act as pollutant carriers and thus provide a rapid transport pathway for strongly sorbing contaminants. To address this problem, we developed a one-dimensional numerical model based on the HYDRUS-1D software package that incorporates mechanisms associated with colloid and colloid-facilitated solute transport in variably saturated porous media. The model accounts for transient variably saturated water flow, and for both colloid and solute movement due to advection, diffusion, and dispersion, as well as for solute movement facilitated by colloid transport. The colloid transport module additionally considers the processes of attachment/detachment to/from the solid phase and/or the air–water interface, straining, and/or size exclusion. Various blocking and depth dependent functions can be used to modify the attachment and straining coefficients. The solute transport module uses the concept of two-site sorption to describe nonequilibrium adsorption–desorption reactions to the solid phase. The module further assumes that contaminants can be sorbed onto surfaces of both deposited and mobile colloids, fully accounting for the dynamics of colloid movement between different phases. Application of the model is demonstrated using selected experimental data from published saturated column experiments, conducted to investigate the transport of Cd in the presence of Bacillus subtilis spores in alluvial gravel aquifer media. Numerical results simulating bacteria transport, as well as the bacteria-facilitated Cd transport, are compared with experimental results. A sensitivity analysis of the model to various parameters is also presented.