The city is drained by three rivers; the West, Mill, and Quinnipiac, named in order from west to east. The West River discharges into West Haven Harbor, while the Mill and Quinnipiac rivers discharge into New Haven Harbor. Both harbors are embayments of Long Island Sound. In addition, several smaller streams flow through the city's neighborhoods, including Wintergreen Brook, the Beaver Ponds Outlet, Wilmot Brook, Belden Brook, and Prospect Creek. Not all of these small streams have continuous flow year-round.

By how many rivers is the city of New Haven drained?