From the Iron Age to the Middle Ages, Axmouth Harbour was the most important harbour in the West of England. The inlet of the estuary of the River Axe was wider and deeper than today, allowing shipping to enter easily and providing a safe haven. Phoenician traders are known to have visited the estuary and it was a significant port in Roman times. The Fosse Way built by the Romans running from Exeter to Lincoln finished at Axmouth, showing how important the port was to the Romans.

However, in the 14th century heavy storms caused part of Haven Cliff to fall and partially block the estuary. The change this cliff fall caused to the flow of the tides built up the shingle bank we see today, significantly narrowing the width of the estuary and leaving the river mouth a narrow channel at the eastern end.

Silt bought down by the river, unable to be carried out to sea as before was deposited in the estuary forming a salt marsh behind the shingle bank.

Before the build up of the shingle bank, shipping moored at Axmouth village, a mile inland and ship anchors have been found as far inland as Axminster.

There were several attempts made to cut through the shingle bank and restore the deep water navigation to the harbour, but the tides soon swept the shingle back defeating all attempts.

The last attempt was made in 1870 by John Hallett who dug a channel and built a quay at the mouth of the river.

The shipping that used this new harbour was able to bring in coal and timber much cheaper than transporting it by land and the port continued to operate commercially until the extension of the rail network  to Seaton in 1868 made the costs of transporting goods by land cheaper than those bought in by sea.

The building of a toll bridge over the river in 1877, 400m from the river mouth to replace the ferry finally stopped any future plans of developing the harbour facilities to enable taller shipping to continue further up river.

Axmouth harbour today is a small, drying harbour dependent upon the tides and used for recreation and by local fishing boats.

The harbour offers access over high water for craft up to 8.5m (30ft) length and 1.5m (4ft) draft. Tidal streams run strongly within the entrance channel and river, particularly on Spring tides when entry and leaving times are critical. Inside, the shelter is good, and the basin is impounded by a bedrock sill.

Visitors can walk on both sides of the harbour; on the western bank is the yacht club with its clubhouse, floating jetties and slipways. Yachts and many other types of small boats are stored on land here particularly during the winter months.

To cross the river, walkers can still use the old toll bridge which was built in 1877. This three arch bridge was one of the first to be built in concrete and is the oldest surviving example of its type. The toll house also built of concrete is on the eastern side of the bridge.