Key waterways in the shire include:
- Campaspe River
- Coliban River
- Deep Creek
- Riddells Creek
- Bolinda Creek
- Jacksons Creek
- Five Mile Creek
Many of the shire’s natural waterways originate in the ranges (higher areas) and flow southeast to the flat, lower parts.
Most of these are tributaries of the Maribyrnong River, which forms to the southeast of the shire. The main flooding risks are associated with tributaries to the Maribyrnong River, particularly Deep Creek and Jacksons Creek.
Deep Creek rises to the east of Woodend on the northern face of the ranges and flows through Lancefield and Romsey before joining with Boyd Creek at Darraweit Guim. It flows out of the shire to the southeast and joins the Maribyrnong River a few kilometres upstream of Bulla. Jacksons Creek flows from above Rosslynne Reservoir, passes through Gisborne and joins the Maribyrnong River a few kilometres downstream from Bulla.
The Campaspe River and in many tributary creeks including the Coliban River, drain the western and northern parts of the shire. The Coliban River originates just outside the shire but passes through its north-western edge. These two large rivers can present flooding issues in Kyneton and Malmsbury, towns in the west of the shire.
Five Mile Creek, one of the Campaspe tributaries causes flooding problems in Woodend.
A small area of the shire to the south of Gisborne is within the Werribee River basin and drains to the Werribee River.
There are a number of reservoirs within the shire, notably Rosslynne Reservoir, just upstream of Gisborne; and Upper Coliban, Lauriston and Malmsbury Reservoirs on the Coliban River near Malmsbury.
Several smaller reservoirs exist near Riddells Creek, on the southern slopes of Mount Macedon. The status of these storages in the lead up to and during a storm event can have a large impact on downstream flood levels and inundation extents.