Transport phenomena in heterogeneous media play a crucial role in numerous engineering applications such as hydrocarbon recovery from shales and material processing. Understanding and predicting these phenomena is critical for the success of these applications. In this dissertation, nanoscale transport phenomena in porous media are studied through physics-based simulations, and the effective solution of forward and inverse transport phenomena problems in heterogeneous media is tackled using data-driven, deep learning approaches. For nanoscale transport in porous media, the storage and recovery of gas from ultra-tight shale formations are investigated at the single-pore scale using molecular dynamics simulations. In the single-component gas recovery, a super-diffusive scaling law was found for the gas production due to the strong gas adsorption-desorption effects. For binary gas (methane/ethane) mixtures, surface adsorption contributes greatly to the storage of both gas in nanopores, with ethane enriched compared to methane. Ethane is produced from nanopores as effectively as the lighter methane despite its slower self-diffusion than the methane, and this phenomenon is traced to the strong couplings between the transport of the two species in the nanopore. The dying of solvent-loaded nanoporous filtration cakes by a purge gas flowing through them is next studied. The novelty and challenge of this problem lie in the fact that the drainage and evaporation can occur simultaneously. Using pore-network modeling, three distinct drying stages are identified. While drainage contributes less and less as drying proceeds through the first two stages, it can still contribute considerably to the net drying rate because of the strong coupling between the drainage and evaporation processes in the filtration cake. For the solution of transport phenomena problems using deep learning, first, convolutional neural networks with various architectures are trained to predict the effective diffusivity of two-dimensional (2D) porous media with complex and realistic structures from their images. Next, the inverse problem of reconstructing the structure of 2D heterogeneous composites featuring high-conductivity, circular fillers from the composites' temperature field is studied. This problem is challenging because of the high dimensionality of the temperature and conductivity fields. A deep-learning model based on convolutional neural networks with a U-shape architecture and the encoding-decoding processes is developed. The trained model can predict the distribution of fillers with good accuracy even when coarse-grained temperature data (less than 1% of the full data) are used as an input. Incorporating the temperature measurements in regions where the deep learning model has low prediction confidence can improve the model's prediction accuracy. / Doctor of Philosophy / Multiphysics transport phenomena inside structures with non-uniform pores or properties are common in engineering applications, e.g., gas recovery from shale reservoirs and drying of porous materials. Research on these transport phenomena can help improve related applications. In this dissertation, multiphysics transport in several types of structures is studied using physics-based simulations and data-driven deep learning models. In physics-based simulations, the multicomponent and multiphase transport phenomena in porous media are solved at the pore scale. The recovery of methane and methane-ethane mixtures from nanopores is studied using simulations to track motions and interactions of methane and ethane molecules inside the nanopores. The strong gas-pore wall interactions lead to significant adsorption of gas near the pore wall and contribute greatly to the gas storage in these pores. Because of strong gas adsorption and couplings between the transport of different gas species, several interesting and practically important observations have been found during the gas recovery process. For example, lighter methane and heavier ethane are recovered at similar rates. Pore-scale modeling are applied to study the drying of nanoporous filtration cakes, during which drainage and evaporation can occur concurrently. The drying is found to proceed in three distinct stages and the drainage-evaporation coupling greatly affects the drying rate. In deep learning modeling, convolutional neural networks are trained to predict the diffusivity of two-dimensional porous media by taking the image of their structures as input. The model can predict the diffusivity of the porous media accurately with computational cost orders of magnitude lower than physics-based simulations. A deep learning model is also developed to reconstruct the structure of fillers inside a two-dimensional matrix from its temperature field. The trained model can predict the structure of fillers accurately using full-scale and coarse-grained temperature input data. The predictions of the deep learning model can be improved by adding additional true temperature data in regions where the model has low prediction confidence.