"flat-bottomed boat" (especially, in military engineering, one to support a temporary bridge over a river), 1670s, from French pontoon, from Old French ponton (14c.) "bridge, drawbridge, boat-bridge; flat-bottomed boat," from Latin pontonem (nominative ponto) "flat-bottomed boat," from pons "bridge" (see pons). Pontoon bridge "roadway supported on pontoons" is recorded by 1778. Related: Pontooneer (n.).
"flat-bottomed, square-ended, mastless river boat," c. 1500, perhaps a local survival of late Old English punt, which probably is from British Latin ponto "flat-bottomed boat" (see OED), a kind of Gallic transport (Caesar), also "floating bridge" (Gellius), from Latin pontem (nominative pons) "bridge" (from PIE root *pent- "to tread, go;" see find (v.)). Or from or influenced by Old French cognate pont "large, flat boat." Compare pontoon.