This study examines a modified permeable pavement system (PPS) for enhanced heavy metal attenuation from stormwater. A laboratory model consisting of six PPS columns has been tested under varying rainfall intensities. The PPS structures are arranged based on the following hypotheses for enhancing heavy metal attenuation: (i) addition of a natural zeolite layer in the subbase for promoting heavy metal attenuation by adsorption and ion exchange; (ii) addition of a bark chip layer as an organic carbon source for promoting biosorption of heavy metals; (iii) maintaining a saturated zone in order to maintain the required humidity level and decrease the level of oxygen for increased biodegradation; and (iv) inclusion of thin sand layers to restrict the transport of oxygen to create an anoxic zone in the PPS and to enhance filtration. Successful treatment of metals such as Ba, Co, Mn, Ni, and Zn has been observed under various rainfall conditions using a conventional PPS. The rainfall intensity greatly influences the attenuation of Al, Cr, Cu, Mo and Sr. During heavy rains through the conventional PPS structure, chromium is found to be leached back into the infiltrate. The results indicate that by changing the subbase material and layer setting, biosorption of heavy metals can be encouraged in the PPS structure. The results of this study suggest that the PPS structure be amended by adding into its subbase a saturated region, an organic carbon donor and thin sand layers for enhanced heavy metal attenuation. Compared to the conventional structure, the proposed structure reduces Cr desorption and improves the attenuation of Al, Cu and Mo.