Koblenz station is served by Zurich S-Bahn line S41, which links Winterthur and Waldshut, and Aargau S-Bahn line S27, which links Baden and Koblenz, with alternate trains continuing to either Waldshut or Bad Zurzach.
In 2007, about 34 trains daily operated as line S41 of the Zürich S-Bahn between Waldshut and Winterthur.