The deeply weathered soil profiles of the ancient landscapes in the Avon River Basin have extensive regional groundwater aquifers and localised unconfined aquifers. Groundwater resources in the Avon Region are generally not suitable for irrigated agriculture due to poor water quality however there are some fresh superficial aquifers with commercial use potential and farm water supply. Some saline groundwater is used for mining.

Groundwater in the Avon River Basin is monitored locally where wells are installed for salinity risk investigations. An inventory of long-term monitoring information of regional aquifers is maintained in 'AQUABASE' which is coordinated by the Department of Environment. Community-based monitoring information is coordinated through 'COMBORES' which is managed by the WA Department of Agriculture. An analysis of monitoring information shows a trend of regional groundwater rise in most areas. Monitoring has also shown groundwater in the region to be acidic.

The regional groundwater aquifers are generally saline, with water quality generally exceeding 30 000 mg/L. Local groundwater flow systems range from fresh to saline. The groundwater processes of the region are well understood although groundwater flow systems of the Avon River Basin have not been mapped. Regional groundwater aquifers between catchments are thought to not be connected. The very low gradient and poorly transmissive soils in the valley floors delay the rate at which groundwater aquifers change but also delays the response to aquifers by groundwater management.

The full potential impact of salinity has been estimated from interpretation of Digital Elevation Models and satellite imagery (the 'Land Monitor Project'). This shows there to be 5.4% of land used for agriculture within the region to be currently effected by salinity but this could eventually increase to 27.5%. This information is consistent with estimates for the region by the National Land and Water Audit (NLWA, 2001). An analysis of the threat of salinity within the Avon Region is provided in the Land resource Supporting Document.