The Gnangara system is the main source of freshwater for Perth, Western Australia. However, aquifers in the region are under severe stress due to a drying climate, intensive pumping and changes in land use. The aim of this study is to apply the mean rainfall cumulative deviation and Mann-Kendall analyses at 77 monitoring bores to investigate the response of the water table to key recharge components. This information is critical for setting new allocation limits and reviewing current policies in the region. Results show that overall there is a good correspondence between water levels and rainfall fluctuations. Areas of groundwater recharge are highly sensitive to climate change and have been severely affected by reduction in rainfall rates in recent years. Further, removal of pine plantations correlated well with a rise in groundwater levels although the effect seems to be temporary. The impact of pumping is mainly observed in vicinities of public-supply borefields. Elsewhere, water table trends show a relative stabilisation indicating that storage still exceeds the influence of rainfall reduction in areas dominated by through flow or groundwater discharge. The study contributes to update the status of the Gnangara groundwater resource, and provides new insights for the sustainable management of one of the main aquifer systems in Australia.