After Corofin, the river flows through Lough Atedaun, Ballyteige Lough, Dromore Lough and Ballyallia Lake. The river then flows through the town of Ennis, where it is crossed by six road bridges, a pedestrian bridge and a railway bridge. There is also a small branch which splits off just north of Ennis and rejoins the main flow to the east of the town.
The river then flows through Lough Inchiquin. Just after this lake, a tributary which has its source at Loughnagowan joins the Fergus. The river then flows along by the village of Corofin.