The Moorabool River drains a catchment of approximately 2,000 km² from the Great Dividing Range near Ballarat southward to its confluence with the Barwon River southwest of Geelong. The river's east and west branches rise in the Wombat State Forest and join near Meredith, after which the river continues through the lower catchment past Batesford and Fyansford before reaching the Barwon.

Paddling the lower Moorabool is a mixed experience. From Batesford Bridge, there is a roughly 3 km section that is relatively straightforward, followed by more demanding terrain as the river approaches the Fyansford area. Reed-choked passages are a recurring feature and frequently require paddlers to haul or drag craft rather than paddle through. Steep banks add to the physical demands in certain stretches. A fallen tree blocking the full width of the river has been reported near the confluence with the Barwon, which can halt progress entirely depending on conditions.

One access point near the Barwon confluence is the Park West boat ramp on Fyans Street in Geelong. Along the lower river, paddlers pass under the Lewis Bandt Bridge on the Geelong Ring Road and can observe the remains of the old trestle bridge that formed part of the Fyansford Cement Works railway, which operated between 1924 and 1966 to carry limestone from Batesford Quarry. The remnants of the conveyor belt infrastructure are also visible along this stretch.

The river supports platypus, cockatoos, and a range of native fish species including tupong, short-finned eel, common galaxias, and Australian grayling. The Moorabool is considered one of the most heavily water-committed rivers in Victoria, with significant extraction for both Ballarat and Geelong water supplies, which affects flow levels and overall river health. Paddlers should anticipate variable water levels and plan accordingly.