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The catchment geomorphology of the Zarqa River in Jordan was investigated using a three-dimensional model and interpretation of geology. There are three major elements that control the Zarqa River catchment and its drainage networks: lithological units, faults and paleovolcanism. The upper catchment is typical of a youthful stage of river development with relatively recent lava fields that have infilled and reduced the original size of the catchment. The lower part of the catchment includes a convex profile probably resulting from the coalescence of knickpoints generated by uplift along the Dead Sea fault. The lower and middle sections of the catchment contain remnants of an older, wider valley, 200–500 m above the present river level, that probably formed during a hiatus in tectonic and volcanic activity from ~ 22 to ~ 13 Ma.