Mudstone pore networks are strong modifiers of sedimentary basin fluid dynamics and have a critical role in the distribution of hydrocarbons and containment of injected fluids. Using core samples from continental and marine mudstones, we investigate properties of pore types and networks from a variety of geologic environments, together with estimates of capillary breakthrough pressures by mercury intrusion porosimetry. Analysis and interpretation of quantitative and qualitative three-dimensional (3D) observations, obtained by dual focused ion beam–scanning electron microscopy, suggest seven dominant mudstone pore types distinguished by geometry and connectivity. A dominant planar pore type occurs in all investigated mudstones and generally has high coordination numbers (i.e., number of neighboring connected pores). Connected networks of pores of this type contribute to high mercury capillary pressures due to small pore throats at the junctions of connected pores and likely control most matrix transport in these mudstones. Other pore types are related to authigenic (e.g., replacement or pore-lining precipitation) clay minerals and pyrite nodules; pores in clay packets adjacent to larger, more competent clastic grains; pores in organic phases; and stylolitic and microfracture-related pores. Pores within regions of authigenic clay minerals often form small isolated networks (<3 μm). Pores in stringers of organic phases occur as tubular pores or slit- and/or sheet-like pores. These form short, connected lengths in 3D reconstructions, but appear to form networks no larger than a few microns in size. Sealing efficiency of the studied mudstones increases with greater distal depositional environments and greater maximum depth of burial.