This study investigated the impact of sediment clogging on the hydraulic performance of porous asphalt (PA) pavements using a novel numerical approach combining the discrete element method (DEM) and computational fluid dynamics (CFD). In particular, image analysis techniques captured the morphology of real aggregates for the 3D appearance information. Then, the information was used to reproduce aggregates and their gradation in asphalt mixes using DEM, including sediments causing clogging of the PA. The samples in the DEM were transferred to CFD for hydraulic performance simulation. DEM samples were prepared with air voids content of 20% and 25%. Clogging particles with different sizes of 0.5 mm and 0.75 mm were used. The study found that clogging particles can move to deeper layers of the PA pavement but have a high potential to be trapped in upper layers and cause clogging issues in the top 5 mm and middle-to-bottom sections. Due to surface clogging, the air voids content for the 20% porosity PA sample was reduced by approximately 2% on average, whereas up to 7% reduction in air voids content was observed for the 25% PA sample. This led to 37.35% and 42.7% reduction in hydraulic permeability, respectively. The reduction in air voids content below 10 mm from the surface is negligible (0.3–0.7% reduction). Due to the clogging development inside the pore structure, the surface runoff on the top of the sample increases by 8.1% for the 20% air voids asphalt sample case and 37.5% for the 25% voids sample. Display omitted •Urban floods generate disruptions on multiple levels to city authorities and people•Permeable road pavements reduce stormwater runoff but can be prone to clogging•3D models of clogged porous pavements are investigated via a novel methodology•DEM-made porous pavements are analysed via multi-phase CFD simulations•Clogging affects the hydraulic performance and surface runoff accumulation