Modeling fluid flow and transport processes in porous media is a relevant topic for a wide range of applications. In water resources problems, this topic presents specific challenges related to the multiphysical processes, large time and space scales, heterogeneity and anisotropy of natural porous media, and complex mathematical models characterized by coupled nonlinear equations. This Special Issue aims at collecting papers presenting new developments in the field of flow and transport in porous media. The 25 published papers deal with different aspects of physical processes and applications such as unsaturated and saturated flow, flow in fractured porous media, landslide, reactive transport, seawater intrusion, and transport within hyporheic zones. Based on their objectives, we classified these papers into four categories: (i) improved numerical methods for flow and mass transport simulation, (ii) looking for reliable models and parameters, (iii) laboratory scale experiments and simulations, and (iv) modeling and simulations for improved process understanding. Current trends on modeling fluid flow and transport processes in porous media are discussed in the conclusion.