All water supplied via the Gascoyne irrigation pipeline is raw untreated non-potable water and is supplied for the irrigation of crops and watering of stock and garden only. 

The water fed into the scheme is sourced from two borefields. The Northern borefield is owned by GWAMCO and operated by GWC and is on the northern bank of the Gascoyne River. The Southern Borefield is managed by the Water Corporation and is on the Southern side of the river.

As part of its licence requirements, GWC collects annual samples from all of the production bores in the Northern borefield and obtains NATA (National Association of Testing Authorities) accredited analysis results on the water produced from this borefield. The Water Corporation also tests the raw water produced from the Southern borefield.