The lower downtown area of Bound Brook has been infamous for flooding of the Raritan River. In September 1999, many structures near the commercial zone were damaged or destroyed by record Raritan floods resulting from Hurricane Floyd. This disaster reinvigorated a long-planned effort called the Green Brook Flood Control Project that would protect Bound Brook from up to a 150-year flooding event from the Raritan River and its tributaries, the Middle Brook and Green Brook that form the western and eastern boundaries of the town. During 1999–2015, the United States Army Corps of Engineers implemented extensive flood control measures to provide protection from future floods.