Summary Throughout the world there are many stressed aquifers used to support irrigated agriculture. The Condamine River catchment (southern Queensland, Australia) is one example of a globally significant agricultural region where groundwater use has exceeded recharge over the last 50 years. There is a high dependence on groundwater in this catchment, because yearly rainfall is highly variable, and actual evapotranspiration often exceeds rainfall. To better manage the aquifer there is a need to correctly conceptualise the primary inputs and outputs of the system, and characterise the lags in system response to all forcings. In catchment models it is particularly important to correctly proportion diffuse (areal) rainfall recharge and to account for the lag between rainfall and recharge at the water table. Throughout large portions of the Condamine Catchment, groundwater levels are now 20 or more metres below the ground surface. This study aimed to better quantify the lag between rainfall and recharge at the water table using the predefined impulse response function in continuous time method (PIRFICT; von Asmuth et al., 2002; von Asmuth, 2012). The PIRFICT method was applied to 255 multi-decadal groundwater level data sets throughout the catchment. Inputs into the modelling include rainfall, irrigation deep drainage, stream water level, evapotranspiration, and groundwater extractions. As an independent check the PIRFICT model derived diffuse recharge estimates are compared to point lysimeter and geochemical recharge estimates in the Vertosol soils within this catchment. It is estimated using the PIRFICT method that in the Condamine Catchment between 1990 and 2012, the mean rain-derived groundwater recharge is 4.4 mm/year. Mean groundwater response from rainfall was determined to be 5.3 years: range 188 days to 48 years. The recharge estimates are consistent with both geochemical and lysimeter point measurements of recharge. It is concluded that where extensive groundwater level and climatic data sets are available the PIRFICT method provides an independent assessment of recharge. Importantly, the PIRFICT method highlights the need to consider the lag between rainfall and recharge at the water table. This lag is often overlooked when calibrating spatial distributed water balance models used to guide groundwater allocations.