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Core Ideas Hydrodynamic and thermal properties of five green roof substrates were determined. Coupled heat and water transport in a hypothetical roof was simulated. The green roof substrates showed a large capacity to store and transport water. Water retention, storage, and organic matter control substrate hydraulic behavior. Green roofs integrate vegetation into buildings, thereby minimizing energy requirements and water runoff. An understanding of the processes controlling water and heat fluxes in green roofs under site‐specific climatic conditions is needed to optimize their benefits. The hydrodynamic and thermal characteristics of substrates and vegetation layers are the primary controlling factors determining water and heat fluxes on green roofs. We characterized the physical, hydrodynamic, and thermal properties of five green roof substrates. We performed coupled heat and water transport numerical simulations to assess the impact of these properties on the hydraulic and thermal performance of a hypothetical roof system. The five substrates showed a large capacity to store and transport water, while their ability to conduct heat was similar to other green roof substrates. Under unsaturated conditions, water retention, storage capacity, and organic matter (OM) content of the substrates controlled the hydraulic and thermal response of each substrate. Our simulation results show that the substrate with the best capacity to store water and to reduce the heat flux through the substrate layer was composed of perlite and peat and had large OM content (30.7%) and saturated water content (0.757 cm3 cm−3). This substrate outperformed the others, probably due to its low thermal conductivity and its large pore space. The dynamic modeling presented in this study can represent the complexity of the processes that are occurring in green roof substrates, and thus it is a tool that can be used to design the configuration of a green roof.