Although compaction affects water and heat transport processes in porous media, few studies have dealt with this problem. This is particularly true for substrates, which are artificial porous media used for engineering and technological solutions, such as in vegetated or green roofs. We propose a methodology to study the effect of substrate compaction on the characterization of physical, hydrodynamic and thermal properties of five green roof substrates. The methodology consists in a parametric analysis that uses the properties of a substrate with known bulk density, and then modifies the substrate properties to consider how compaction affects water and heat fluxes. Coupled heat and water transport numerical simulations were performed to assess the impact of the changes in the previous properties on the hydraulic and thermal performance of a hypothetical roof system. Our results showed that compaction reduced the amplitude of the fluctuations in the volumetric water content daily cycles, increasing the average water content and reducing the breakthrough time of the green roof substrates. Compaction changes the thermal behavior of the green roof substrates in different ways for each substrate due to the dependence of the air, water and soil fraction of each substrate.