Permeable pavement systems are a sustainable urban drainage technique created with a highly porous base and subbase. This study first analyses the hydraulic performance of several new permeable pavement systems based on 189 experimental hydrographs. In addition, the analysis explores the influence of rain intensity, slope, and, as a novelty, individual layers. Analysed variables were outflow peak, time to peak, and time to specific cumulative discharges. Secondly, based on the experimental hydrographs, the study explores the performance of the permeable pavement module defined in the Storm Water Management Model, carried out in two steps. First, single-layer outflows were used to calibrate parameter values that could not be measured physically, using the differential evolution algorithm and Nash–Sutcliffe model efficiency coefficient as an objective function. Later, complete layout hydrographs were tested without calibration, and model performance was checked. Results show that the superficial permeable interlocking paver layer provides a notably higher retention capacity than the porous asphalt mixture. Individual modelling results show that the soil layer definition is inappropriate for gravel-type layers, even with a geotextile. Despite this, complete section performance is quite good without calibration if the soil layer is not selected on the model. These results are expected to reduce modelling uncertainty, especially when no calibration data is available.