Both the composition and distribution of the lithocomponents within an aquifer impact hydrophobic organic compound (HOC) transport. Using samples from the sandy, low fraction organic carbon content (f(oc)~0.02%) Borden aquifer, we demonstrate how HOC sorption is controlled by the carbonaceous matter (CM) associated with calcareous sedimentary lithocomponents. Two-point isotherms using perchloroethene (PCE) as a sorbate showed that medium-grained lithofacies have a broader range of K(f) (Freundlich coefficient), 1/n (Freundlich parameter) and f(oc) than fine-grained facies. Dual-mode (linear+Freundlich) sorption modeling, fraction inorganic carbon (f(ic)) and laboratory analyses confirm that both the magnitude and variability of PCE K(d) (sorption distribution coefficient) in the Borden aquifer are controlled by the presence of heterogeneous CM in dark and very dark carbonate lithocomponents. Laboratory analyses and model results confirmed that the CM type controlling PCE sorption behavior in the Borden aquifer is in a condensed form, likely kerogen, contained within the carbonate matrix of the grains. The dark carbonate grains comprise a small proportion of the aquifer sediment (≪1%) and are found predominantly in medium-grained lithofacies in the Borden aquifer. These results show that increased heterogeneity, HOC mass storage and sorption nonlinearity associated with medium-grained lithofacies impact HOC transport in historically contaminated sedimentary aquifers.