Peatlands are wetlands that provide important ecosystem services including carbon sequestration and water storage that respond to hydrological, biological, and biogeochemical processes. These processes are strongly influenced by the complex pore structure of peat soils. We explore the literature on peat pore structure and the implications for hydrological, biogeochemical, and microbial processes in peat, highlighting the gaps in our current knowledge and a path to move forward. Peat is an elastic and multi-porous structured organic soil. Surficial (near-surface) peats are typically dominated by large interconnected macropores that rapidly transmit water and solutes when saturated, but these large pores drain rapidly with a reduction in pore-water pressure, and disproportionally decrease the bulk effective hydraulic conductivity, thus water fluxes that drive ecohydrological functions. The more advanced state of decomposition of older (deeper) peat, with a greater abundance of small pores, restricts the loss of moisture at similar soil water pressures and is associated with higher unsaturated hydraulic conductivities. As evaporation and precipitation occur, peat soils shrink and swell, respectively, changing the hydrological connectivity that maintain physiological processes at the peat surface. Due to the disproportionate change in pore structure and associated hydraulic properties with state of decomposition, transport processes are limited at depth, creating a zone of enhanced transport in the less decomposed peat near the surface. At the micro-scale, rapid equilibration of solutes and water occurs between the mobile and immobile pores due to diffusion, resulting in pore regions with similar chemical concentrations that are not affected by advective fluxes. These immobile regions may be the primary sites for microbial biogeochemical processes in peat. Mass transfer limitations may therefore largely regulate belowground microbial turnover and, hence, biogeochemical cycling. For peat, the development of a comprehensive theory that links the hydrological, biological, and biogeochemical processes will require a concerted interdisciplinary effort. To that end, we have highlighted four primary areas to focus our collective research: 1) understanding the combined and interrelated effects of parent material, decomposition, and nutrient status on peat pore connectivity, macropore development and collapse, and solute transport, 2) determining the influence of changing pore structure due to freeze-thaw or dewatering on the hydrology and biogeochemistry, 3) better elucidating the non-equilibrium transport processes in peat, and 4) exploring the implications of peat’s pore structure on microbiological and biogeochemical processes.