The topography of Franklin Township is generally characterized by flat to gently rolling terrain.
Elevations are lowest along the edges of the township where the Raritan and Millstone rivers converge, sitting near sea level to 40 feet. The interior of the township rises into gentle hills, reaching maximum elevations of around 250 feet above sea level. Because it is surrounded by two major rivers, the township features significant flood plains, which are prone to inundation during major rain events. The western border is defined by the flat, linear topography of the D&R Canal and its accompanying towpath.

