Within the scope of the conducted experiment the authors analysed the efficiency of runoff reduction by the system of extensive type green roofs. The observations were based on storm events in the area of Lower Silesia at the Agro and Hydrometeorology Station Wrocław-Swojec. The authors analysed the thickness of plant substrate, and also estimated the quality of runoff waters under the conditions of periodic atmospheric deposition. Also considered were such indicators as electrolytic conductivity, N, NO3−, NO2−, NH4+, P, PO43−. The experiment included roof substrates designed in two variants, with known hydraulic and physical properties of the soil material. The analysis was performed for models with vegetation layer based on pumice and zelolite, covered with five plant species from the sedum family. The modelling of the hydraulic properties was conducted with variably saturated medium, using the Hydrus 1D software. The performance of systems with primary layer thickness of 11 cm and 9, 8, 7, 6 and 5 cm was estimated. The designed models reduced the average peak flows to 89%, and in addition they caused a delay in the initiation of the runoff which was dependent on the intensity and distribution of rainfalls in time, and on the initial moisture of the profiles. Simulations, performed for variable substrate thickness, permit the conclusion that in the case of thin-layer profiles (5 cm), the relative retention index was decidedly lower and amounted to 35.9% for the substrate with zeolite (originally 60.6%) and 41% for the substrate with pumice (originally 65.7%). In the case of total nitrogen and phosphates, statistical analysis revealed significant differences (p < 0.05) in relation to specific concentrations in the rainwater and in the control surface. The total nitrogen in the runoff from the green roof was nearly twice as high as that in the rainwater and amounted to, on average, 8.3 mg L−1.