Green roofs are constructions made of different layers, each serving a dedicated function. Substrates and materials used in their composition are essential from the point of view of rainwater retention and plant development, but they may have an adverse effect on runoff quality. Literature studies show that phosphorus and heavy metals are of main importance. The total roofs area covered with green increased in the last years in cities as they are efficient in retention of rainwater and delaying of the runoff, therefore, protecting the cities against floods. As green roofs filtrate a significant amount of rainwater, materials used in substrates composition should be carefully selected to protect urban receivers against pollution. The aim of this study was to assess phosphorus and heavy metals leaching from different green roof substrates and their components with the focus on green roof runoff quality. Both commercially made green roof substrates and often used compounds (construction aggregates) were tested in laboratory batch tests for P, Cu, Ni, Cd, and Zn content in extracts. Based on the results of this study, it could be emphasized that a large part of commonly used construction aggregates can be a source of phosphorus, some also can release elevated values of nickel. Therefore, the materials should be carefully tested before use in the green roof substrate composition, not only for their physical properties reflecting water retention capacity, but also for chemical composition.