Groundwater recharge is critical for sustainable water resource planning and modelling fluid and contaminant transport within th e subsurface. Unfortunately, direct groundwater measurements are often too short to investigate long-term trends for many regions in Australia. Over the past, a number of methods have been developed to estimate groundwater recharge over different temporal and spatial scales. Among the most widely used techniques for estimating recharge, the water table fluctuation (WTF) method has been applied in numerous studies. In this study, we use the WTF method to estimate annual groundwater recharge at 438 groundwater monitoring bores in South Australia and analyse long-term annu al groundwater recharge trends using the nonparametric Mann -Kendall trend test. The results indi cate that the spatially averaged annual groundwater recharge has declined significantly with a trend of -0.92 mm/year for the period 1970- 2012. Similar trend tests for the 237 groundwater monitoring bores with longer data records exhibit that 161 bores have downward trends of which 103 bores are statistically significant, whereas 44 bores have upward trends and 15 of them are statistically significant. Moreover, a linear extrapolation of annual groundwater recharge trend suggests that the m ean will reach the lowest recorded annual recharge in history (2006 drought) by 2058 if the recent clima tic trends continue over a longer peri od, indicating a potential threat to the hydrological and ecological regimes. Furthermor e, the correlation analysis demonstrates that the dominating downward trends in annual groundwater rech arge are affected by the large-scale hydroclimate variables (e.g. rainfall) in South Australia.