It runs through the states of North Rhine-Westphalia and Lower Saxony, and discharges into the Dollart Bay which is part of the Wadden Sea.

Near Emden, it flows into the Dollard bay (a national park) and then continues as a tidal river towards the Dutch city of Delfzijl.

Between Emden and Delfzijl, the Ems forms the border between the Netherlands and Germany and was subject to a mild dispute: the Dutch believed that the border runs through the geographical centre of the estuary, whereas the Germans claimed it runs through the deepest channel (which is close to the Dutch coast).

[2][3] It became an active issue in late July 1914, when the Imperial German government began plans to mine the whole of the estuary that they claimed, in preparation for the launching of the Great War.

The Dutch envoy in Berlin, Wilem Alexander Frederik Baron Gevers, tactfully announced the boundary was uncertain, and that the dispute was "opgeschort", which could mean either "suspended" or "resolved", depending on the context.

The Dollart Bay near Emden did not exist until 1277,[5] when a catastrophic storm surge flooded 43 parishes and killed an estimated 80,000 people.

Construction of canals in more modern times connected the Ems to other waterways, opening it as a highway of industrial transportation.