The harvesting, storage and reuse of stormwater from permeable pavement reservoirs provides an opportunity to alleviate water shortages in urban areas. Reservoirs may be filled with a range of basecourse aggregate materials that provide structural support to the pavement. The materials have the potential to affect the quality of stored water. This research investigated changes in water quality when water was stored in two types of basecourse aggregate. Synthetic stormwater was placed in permeable pavement reservoir models filled with dolomite aggregate or quartzite aggregate or control reservoirs with no aggregate. The influence of residence time was investigated by monitoring stored water quality for up to 144 h. Conductivity and pH increased in both aggregate-filled reservoirs. Total suspended solids and turbidity also increased in the aggregate-filled reservoirs, before falling to levels significantly lower than the control reservoirs. Levels of phosphorous and organic nitrogen were significantly lower in the aggregate-filled reservoirs after 144 h. Total zinc, copper and lead were reduced by 94–99% in the aggregate-filled reservoirs compared with the controls after 144 h storage.