The Geelong City area is split between the Moorabool River Basin in the northern half, and the Barwon River Basin in the south. The area contains part of the lower Moorabool River, connecting with the Barwon river near Fyansford, west of Geelong’s urban centre. The Barwon River stretches south, with Waurn Ponds creek meeting the Barwon River in the south of the area. The Geelong City area also contains part of Hovells Creek separate to its other major waterways, flowing from the north past the town of Lara, into Limeburners Lagoon State Nature Reserve (part of the Port Phillip Bay (Western Shoreline) and Bellarine Peninsula Ramsar Site), into Corio Bay. All the waterways in the Geelong City area were assessed as being in very poor condition in the Index of Stream Condition in 2010.

The Geelong landscape system has part of the Barwon River flowing through it, which is part of a globally important bird conservation habitat, as well as habitat for Growling grass frog (nationally endangered).

The very poor condition of hydrology in the lower Barwon River and of the Barwon River Basin is attributed to reservoir operations in the Upper Barwon and Upper Moorabool areas that supply water to Geelong, Ballarat and neighbouring basins, and to the presence of the tidal barrage downstream of the reach.

The Moorabool River’s reach in the area has an extremely modified flow regime, often experiencing extended periods of low flow throughout summer and winter, as well as zero flow periods during summer.

Corangamite Waterwatch, a citizen science volunteer program, regularly monitors water quality parameters at many sites across the catchment. Data collected shows that as the Barwon River makes its way into Geelong after the confluence with the Moorabool River, the water quality is marginally degraded. High dissolved oxygen levels over summer indicate potential algal growth. In the past this section of the Barwon River through Geelong often experienced algal blooms over summer. The Jerringot and Pakington St wetlands on the banks of the Barwon River receive urban stormwater runoff. High phosphorus levels are common and may encourage macrophyte and algal growth which potentially creates oxygen troughs over the summer to autumn seasons and raises pH levels and ammonia toxicity. Macroinvertebrates indicate the water quality to be moderately impacted. The Waurn Ponds Creek, a tributary of the Barwon River, also displays poor water quality and at times of low flows has the potential for saline groundwater intrusion. The creek also has high phosphorus and turbidity levels. At the site there is a good cover of riparian vegetation, however there is potential for further bank erosion in this incised stream and the instream habitat for aquatic organisms is degraded. Macroinvertebrates indicate the creek is mildly impacted.

As the Barwon River enters the estuary at the lower breakwater the water quality is relatively healthy. During winter flooding, flows in the catchment completely flush the estuary of saltwater and becomes freshwater dominated. High turbidity occurs at this time, however is short lived and the tidal salt wedge pushes back up the estuary. Occasionally over summer as river flow declines, saltwater dominates.

The water quality in Hovells Creek over time was relatively healthy for an urban stream, maintaining low salinity, stable pH and mostly low turbidity. In recent times turbidity levels have increased, particularly in 2019, indicating an increase in sediment entering the stream – possibly due to unrestricted stock access, greatly reduced riparian vegetation in the catchment and urban development around Lara. Increases in sediment can smother habitat for aquatic macroinvertebrates and reduce the amount of light penetrating the water for submerged aquatic vegetation. Low dissolved oxygen levels indicate the waterway is impacted by high instream oxygen demand. A notable increase in nutrients such as phosphorus is also evident at times of increased turbidity. This is likely linked to urban runoff during times of high rainfall and farming practices in the catchment, whereby the phosphorus is imported to waterways attached to soil particles; when this makes its way into the waterways it has the potential to increase the growth of aquatic plants and even stimulate algal blooms. These have the potential to impact on the environment downstream.

The water quality in Cowies Creek was marginal. Urban development in the catchment may have contributed to this. , At times of reduced river flow over summer, salinity levels increase, possibly due to the ingression of saline ground water. At times of high rainfall and increased river flow, salinity reduces – however during these times turbidity and phosphorus levels increase. Turbidity and phosphorus levels have remained relatively low since 2014. This is common in urban waterways as pollutants enter via stormwater runoff during high rainfall events. The impact of increased nutrient levels within the creek can result in excessive aquatic macrophyte and potential algal growth. The dissolved oxygen levels in the water suggest this is occurring particularly over the warmer months. Low dissolved oxygen levels indicate there to be high instream oxygen demand at times. In Cowies Creek, the frequency of monitoring has reduced, but shows an overall improvement since 2014.