Nanoporous media consist of homogeneous or heterogeneous porous material in which a significant part of the pore size distribution lies in the nanometer range. Clayey rocks, sediments or soils are natural nanoporous media, and cementitious materials, the most widely used industrial materials in the world, are also nanoporous materials. Nanoporous materials also include compounds present at the interface between non-porous solids and a aqueous solution. For example, hydrous silica gel coatings are interfacial nanoporous media that control the weathering rates of silicate glasses and minerals (Bourg and Steefel 2012). The understanding of the reactive and transport properties of these interfacial phases is essential to our global understanding of the long-term evolution of natural systems, such as soil formation (Navarre-Sitchler et al. 2011), nutrient cycling in the oceans (Loucaides et al. 2010), and engineered applications, such as the prediction of radionuclides release in high-level radioactive waste disposals (Grambow 2006; Collin et al. 2018a,b; Frugier et al. 2018). In colloidal suspensions, the aggregation of nanoparticles can also lead to the formation of nanoporous aggregates in which the bulk properties of nanoparticles are strongly influenced by the surrounding nanopores. For example, the dynamics of contaminant retention in ferrihydrite aggregates can be slowed by diffusional processes in the into/out of aggregates (Beinum et al. 2005). The bulk fluid transport properties and the in situ chemical reactivity properties of nanoporous media are notoriously difficult to characterize. Because of their large specific surface area, most of the fluid volume in nanoporous media is influenced by the close proximity of mineral1 surfaces, which explains the very low transmissivity of these materials. As a consequence, the experimental characterization of their permeability requires special techniques (Neuzil and Person 2017). Also, the large specific surface area of nanoporous material provides them with very high adsorption capacity. The strong adsorption and resulting retardation of many contaminants by nanoporous material make them ideal for use in natural or engineered barrier systems or in filtration technologies. A good understanding of their chemical reactivity coupled to their transport properties is necessary to predict the long-term evolution of these properties of interest as a function of a range of physical and chemical conditions and processes. In this regard, reactive transport modeling can help bridging the gap between current process knowledge and predictions of the long term evolution of natural and engineered nanoporous materials in geological and industrial settings. However, nanoporous media exhibit a remarkable array of macro-scale properties with marked departures from those observed in “conventional” porous media such as permeable aquifers, for the study of which reactive transport models and codes have been historically developed. These properties arise from the interactions of charged mineral surfaces with water and solutes present in the nanopores, which leads to coupling between flux terms. These couplings manifest themselves in macroscopic observations that have intrigued geologists for more than one century, such as geologic ultrafiltration, i.e., the accumulation of solutes on the inflow side of clay-rich lithologies (Lynde 1912; Neuzil and Person 2017). The vast majority of published reactive transport studies dealing with clay and cement materials are related to the evaluation of the long-term stability of surface and underground radioactive waste storage systems (Claret et al. 2018 and references therein; Bildstein et al. 2019, this volume, and references therein). In these types of simulation, the modeling effort has been focused primarily on the reactivity of the nanoporous materials rather than on their transport properties. Traditionally, Fickian diffusion has been typically considered, i.e., without taking into account advection, and without taking into account the anomalous transport properties of nanoporous media. In the last decade, special capabilities have been developed in a limited number of reactive transport codes that make them able to model part of these unconventional properties, with consideration of coupled processes that go beyond the traditional coupling between advective flow, dispersion, diffusion and reactions. The present chapter reviews these recent developments and explores the need to develop additional code capabilities to encompass relevant properties of nanoporous media in a holistic model from the micro-continuum to macro-continuum scales. The micro-continuum scale is restricted here to the definition given by Steefel et al. (2015b), i.e., a scale with resolution intermediate between true pore scale models and macro-continuum models, and in which parameters and properties such as permeability or reactive surface area need to be averaged or upscaled in some fashion. This corresponds to the matrix domains in the hybrid micro-continuum scale description defined by Soulaine et al. (2016, 2018), in which flow in true pore scale domains are described with the Navier–Stokes equation, whereas flow in matrix is described with Darcy's Law. Clayey materials are, by far, the most studied nanoporous media using reactive transport modeling. Consequently, most of the examples described in this chapter deal with clays. Also, this review is limited to coupled processes in water-saturated nanoporous media. This chapter begins with a description of nanoporous media and the semi-permeable behavior that arises from the combination of their microstructure and their surface properties. Then, non-coupled and coupled transport processes in porous media are defined. In the next section, a quantitative description of the ion concentration distribution in the porosity of nanoporous materials is given, together with the approximations used in reactive transport codes to calculate it effectively. The reactive transport treatment of coupled transport processes is then described in the two last sections, starting from a description of transport in the diffusive regime, and ending with the challenges associated with the consideration of advective flow in nanoporous media.