1520s, from Middle Dutch wagen, waghen, from Proto-Germanic *wagnaz (cf. Old English wægn, Modern English wain, Old Saxon and Old High German wagan, Old Norse vagn, Old Frisian wein, German Wagen), from PIE *woghnos, from *wegh- "to carry, to move" (cf. Sanskrit vahanam "vessel, ship," Greek okhos, Latin vehiculum, Old Church Slavonic vozu "carriage, chariot," Russian povozka, Lithuanian vazis "a small sledge," Old Irish fen, Welsh gwain "carriage, cart;" see weigh).
In Dutch and German, the general word for "a wheel vehicle;" English use is a result of contact through Flemish immigration, Dutch trade, or the Continental wars. It has largely displaced the native cognate, wain. Spelling preference varied randomly between -g- and -gg- from mid-18c., before American English settled on the etymological wagon, while waggon remained common in Great Britain. Wagon train is attested from 1810. Phrase on the wagon "abstaining from alcohol" is 1904, originally on the water cart.