Distribution of alkanes and water in organic pores of shale, referred to as kerogen, is essential information required for estimation of shale-reservoir oil- and gas-in-place, adsorption of hydrocarbon, and fate of frac-water. A practical modeling approach is presented for proper description of the kerogen pore systems with different mixed wettability, surface roughness, tortuous paths, and material disorder. Three kerogen models, namely activated kerogen, kerogen free of active sites, and grapheme-slit pore, with proper surface-oxidized functional groups and high-temperature-and-pressure maturation, are constructed by simulation. Distribution of octane and water in the organic pores of these models is predicted by molecular dynamics simulation. Comparison of results reveals the importance of accurate characterization of kerogen pore systems by particular pore morphology, surface activation, and pore size. The improved kerogen models provided here are shown to determine the placement, distribution, and trapping of frac-water in shale depending on the maturity of the kerogen within organic-rich shales.