Due to the many benefits offered by Green Roofs Systems (GRS), such as: energy savings in buildings and reducing urban heat island, to mention some, these have been extensively studied in recent years. Many theoretical and experimental studies have been conducted to determine the potential of the GRS as passive cooling systems in buildings. However, most of the experimental studies are applicable only to GRS in question and the existing mathematical models to predict the heat flux, through the various layers of biotic and abiotic materials that make up the GRS, assume that these layers are formed by homogeneous materials and not consider that these may be heterogeneous media. In this work is considered that some of the layers that make up GRS are heterogeneous, as the green layer is formed by plants and air or the substrate layer is formed by land and water; thus, a heat transfer model for GRS is proposed that consider biphasic media, and non-conventional boundary condition for coupling the GRS layers are proposed; this model allows further study of heat transfer through heterogeneous media, especially in GRS. The model is verified with data published and experimental data obtained in the Controlled Environment Laboratory of the Universidad Autonoma Metropolitana-Iztapalapa. (C) 2017 Elsevier B.V. All rights reserved.