Groundwater is an important contributor to irrigation water supplies. The time lag between withdrawal and the subsequent impacts on the river corridor presents a challenge for water management. We highlight aspects of this challenge by examining trends in the groundwater levels and changes in groundwater management goals for the Namoi Catchment, which is within the Murray–Darling Basin, Australia. The first high-volume irrigation bore was installed in the cotton-growing districts in the Namoi Catchment in 1966. The development of high-yielding bores made accessible a vast new water supply, enabling cotton growers to buffer the droughts. Prior to the development of a groundwater resource it is difficult to accurately predict how the water at the point of withdrawal is hydraulically connected to recharge zones and nearby surface-water features. This is due to the heterogeneity of the sediments from which the water is withdrawn. It can take years or decades for the impact of groundwater withdrawal to be transmitted kilometres through the aquifer system. We present the analysis of both historical and new groundwater level and streamflow data to quantify the impacts of extensive groundwater withdrawals on the watertable, hydraulic gradients within the semi-confined aquifers, and the movement of water between rivers and aquifers. The results highlight the need to monitor the impacts of irrigated agriculture at both the regional and local scales, and the need for additional research on how to optimise the conjunctive use of both surface-water and groundwater to sustain irrigated agriculture while minimising the impact on groundwater-dependent ecosystems.