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Heterogeneity of soil hydraulic (e.g., hydraulic conductivity (KS), porosity (θS)) and chemical (e.g., solid-phase adsorption (Kd)) properties complicates contaminant transport by creating spatial variability in sources of contaminant leaching. There is a knowledge gap on the effect of the interplay between these properties on the retardation and transport of per- and polyfluoroalkyl substances (PFAS) with different properties including carbon–fluorine chain-length and functional groups even in water-saturated conditions. Breakthrough curves have been used to evaluate PFAS transport behavior through heterogeneous media, including arrival time, maximum concentration, and tailing behavior. Contaminant mass flux reduction and mass removal correlations are also compared using numerical modeling to characterize PFAS transport through different source zones within a two-domain, heterogeneous system with comparison to homogeneous scenarios under water-saturated conditions. With heterogeneous properties, model sensitivity to KS was the highest among the other parameters and was controlled by the KS ratio between the different soils. The PFAS models in the homogeneous and heterogeneous scenarios were both sensitive to θS, depending on PFAS chain length. However, long-chain PFAS were less sensitive to θS variability compared to short-chain PFAS due to their higher Kd. The homogeneous and heterogeneous scenarios were equally sensitive to Kd variability, which was dependent on PFAS chain length.