We present the state-of-the-art of theoretical modeling, molecular simulation, and coarse-graining strategies for the transport of gases and liquids in nanoporous materials (pore size 1-100 nm). Special emphasis is placed on the transport of small molecules in zeolites, active carbons, metal-organic frameworks, but also in nanoporous materials with larger pores such as ordered and disordered mesoporous oxides. We present different atomistic and mesoscopic methods as well as available theoretical formalisms to describe such a complex problem. Attention is given to the investigation of different molecular transport coefficients─including the self, collective and transport diffusivities─but also to the determination of free energy barriers and their role in overall adsorption/separation process rates. We further introduce other available approaches such as hierarchical simulations and upscaling strategies. This review focuses on simple fluids in prototypical nanoporous materials. While the phenomena covered here capture the main physical mechanisms in such systems, complex molecules will exhibit additional specific features. For the sake of clarity and brevity, we also omit multicomponent systems (e.g., fluid mixtures, electrolytes, etc.) and electrokinetic effects arising when charged systems are considered (ionic species, charged surfaces, etc.), both of which add to the complexity.