The use of green roofs, a low-impact development practice, can be an effective means of reducing direct runoff in urban centers. Green roof modeling can enable efficient design by preliminarily grasping the behavior of the green roof system according to specific configurations. In this study, we aimed to find appropriate evapotranspiration and parameter optimization schemes for HYDRUS-1D, a commonly used modeling tool for green roofs. Comparative studies of this sort in the context of green roof runoff modeling have not been conducted previously and are important in guiding users to overcome the difficulties of choosing the right numerical schemes for an accurate prediction of runoff from a green roof. As a study site, the Portland Building Ecoroof in Portland, Oregon, USA, was chosen, as green roof configurations and observed data for climate and runoff were available. From the simulation results of the runoff volume, the Blaney–Criddle method, which was considered an alternative, was found to be appropriate for calculating evapotranspiration from a green roof (R2 = 0.82) relative to the Hargreaves method built in HYDRUS-1D (R2 = 0.46). In addition, this study showed that the optimization method using the harmony search algorithm, which was proposed as an alternative optimizer, was better (R2 = 0.95) than that of the HYDRUS-1D’s own optimization module (R2 = 0.82) in calibrating HYDRUS-1D for green roof runoff. The findings are thought to be useful in guiding modelers who are considering using HYDRUS-1D for green roof runoff simulations.