U–Pb ages of detrital (n = 2391) and magmatic (n = 170) zircon grains from the Harz Mountains were obtained by LA-ICP-MS for provenance studies and absolute age dating. Results point to a complete closure of the Rheic Ocean at c. 419 Ma. A narrow Rhenish Seaway then re-opened in Emsian to mid-Devonian time (c. 390–400 Ma). Devonian sedimentary rocks of the Harz Mountains were deposited on the northwestern (Rheno-Hercynian) and on the southeastern (Saxo-Thuringian) margins of the Rhenish Seaway. A new U–Pb zircon age from a plagiogranite (329 + 2 Ma) within a harzburgite makes the existence of oceanic lithosphere in the Rhenish Seaway probable. The Rhenish Seaway was completely closed by Serpukhovian time (c. 328 Ma). Existence of a terrane in the seaway is not supported by the new data. Provenance studies and spatial arrangement allow reconstruction of the thin-to thick-skinned obduction style of the Harz Mountains onto the southeastern margin of East Avalonia (Rheno-Hercynian Zone) during the Variscan orogeny. Detrital zircon populations define Rheno-Hercynian and Saxo-Thuringian nappes. Intrusion of the granitoid plutons of the Harz Mountains occurred in a time window of c. 300 to 295 Myr and constrained the termination of Variscan deformation.