Ubiquitous observations of channelised fluid flow in the form of pipes or chimney-like features in sedimentary sequences provide strong evidence for significant transient permeability-generation in the subsurface. Understanding the mechanisms and dynamics for spontaneous flow localisation into fluid conductive chimneys is vital for natural fluid migration and anthropogenic fluid and gas operations, and in waste sequestration. Yet no model exists that can predict how, when, or where these conduits form. Here we propose a physical mechanism and show that pipes and chimneys can form spontaneously through hydro-mechanical coupling between fluid flow and solid deformation. By resolving both fluid flow and shear deformation of the matrix in three dimensions, we predict fluid flux and matrix stress distribution over time. The pipes constitute efficient fluid pathways with permeability enhancement exceeding three orders of magnitude. We find that in essentially impermeable shale, vertical fluid migration rates in the high-permeability pipes or chimneys approach rates expected in permeable sandstones. This previously unidentified fluid focusing mechanism bridges the gap between observations and established conceptual models for overcoming and destroying assumed impermeable barriers. This mechanism therefore has a profound impact on assessing the evolution of leakage pathways in natural gas emissions, for reliable risk assessment for long-term subsurface waste storage, or CO2 sequestration.