Green roofs are among the important green infrastructures which decrease the negative impacts of urbanization. In this study, the green roof modeling capability of U.S. Environmental Protection Agency Storm Water Management Model (EPA SWMM) is evaluated and the modeling methods used in EPA SWMM, which need improvements, are determined. In particular, the drainage flow, which is originally calculated with Manning's equation in SWMM, is improved by introducing the drainage mat void thickness and adapting a new value for the exponential coefficient of depth in the equation. In addition, the capability of the percolation equation is further investigated, i.e., the value of the coefficient of the exponential function of soil moisture content that considers the percolation through the soil layer is determined for different substrates using the existing unsaturated hydraulic conductivity and soil moisture content data from steady-state tests. A comparison of the improved equation of drainage flow results with the existing experimental data shows that the improved equation represents the drainage flow more accurately than the one used in EPA SWMM.