The pore structure of Salem limestone is investigated, and conclusions regarding the effect of the pore geometry on modeling moisture and contaminant transport are discussed based on thin section petrography, scanning electron microscopy, mercury intrusion porosimetry, and nitrogen adsorption analyses. These investigations are compared to and shown to compliment permeability and capillary pressure measurements for this common building stone. Salem limestone exhibits a bimodal pore size distribution in which the larger pores provide routes for convective mass transfer of contaminants into the material and the smaller pores lead to high surface area adsorption and reaction sites. Relative permeability and capillary pressure measurements of the air/water system indicate that Salem limestone exhibits high capillarity end low effective permeability to water. Based on stone characterization, aqueous diffusion and convection are believed to be the primary transport mechanisms for pollutants in this stone. The extent of contaminant accumulation in the stone depends on the mechanism of partitioning between the aqueous and solid phases. The described characterization techniques and modeling approach can be applied to many systems of interest such as acidic damage to limestone, mass transfer of contaminants in concrete and other porous building materials, and modeling pollutant transport in subsurface moisture zones.