Rising near the village of Clyst William near Cullompton, the river runs west and southwest, flowing through the settlements of Norman's Green, Plymtree, Clyst Hydon, Clyst St. Lawrence, Westwood, emerging in the Clyst Valley.
From there, the river goes southward through Broadclyst, West Clyst, Clyst Honiton, Clyst St. Mary and Clyst St. George, eventually flowing into the Exe estuary at Bowling Green Marsh, immediately south of the port of Topsham near Exeter.
In 2011 work started on a new £500,000 cycle and pedestrian bridge crossing the River Clyst at Fishers Mill, Topsham, forming part of the Sustrans’ National Cycle Network [NCN]. The bridge feeds into the Exe Estuary Trail, part of NCN2. A 50-metre elevated timber boardwalk was planned across the salt marshes and flood plain with a main bridge spanning 28 metres across the river. The new bridge is downstream from an existing narrow Grade II Listed masonry highway bridge.
In winter, the flood plain attracts large flocks of Brant geese and Canada geese. On the north side of the Clyst, just west of the Exmouth railway line, is Bowling Green Marsh, a small RSPB reserve with a hide (SX971877).
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