Channelised fluid flow within high-permeable chimneys or pipes is ubiquitously and worldwide observed from the earth interior to the shallow subsurface and occurs at various length and time scales. These flow pathways allow for fast vertical fluid migration in natural settings and reservoir operations. However, no current model explains and predicts how, when and where these chimneys are formed. I will present a physical mechanism of such chimney formation using novel high-resolution two-phase numerical calculations in three-dimensions. To model the chimney evolution in deforming porous media we developed a parallel numerical application that solves poro-mechanics coupled to nonlinear fluid flow. Our results confirm that a strong coupling between solid deformation and fluid flow provides a viable mechanism for chimney formation. We validate our model using the important quantity of available geophysical data for the shallow subsurface, together with model parameters relevant for sedimentary rocks. Our model reproduces natural observations and their main characteristic features. These a ccurate predictions are vital to understand the formation of potential leakage pathways and are a prerequisite for reliable risk assessment in long term storage.