The River Axe rises from the ground at Wookey Hole in the north of the county. The source of the river is water draining from the high ground of the Mendips. The geology of the area is limestone and the water proceeds down to Wookey hole in a series of underground channels that have eroded through the soft limestone.
From Wookey Hole the river flows through a ravine and then west through the village of Wookey. At Wookey the River splits into two channels with the Lower River Axe ( a former millstream) running past to the south of the village west towards Henton and then onto Panborough Moor where it joins a series of rhynes and drains supplying water to the wetland in the area. The Lower River Axe then runs north along the west most edge of Knowle Moor whilst the River Axe continues west through the same moor. The two channels meet again on the boundary between Knowle and Panborough Moors.