The permeable reactive weir (PRW) is a device that removes pollutants from surface water to improve aquatic habitats. It is comprised of an outer wall that holds replaceable filter media to address site-specific water quality concerns. PRWs control water flow through ports and can be customized to site conditions, installed in various waterways. They may be used in series or parallel with engineered streambeds below to further treat water through the hyporheic zone.