The groundwater-dependent ecosystem in the Gnangara region is confronted with great threats due to the decline in groundwater level since the 1970s. The aim of this study is to apply multiple trend analysis methods at 351 monitoring bores to detect the trends in groundwater level using spatial, temporal and Hydrograph Analysis: Rainfall and Time Trend models, which were applied to evaluate the impacts of rainfall on the groundwater level in the Gnangara region, Western Australia. In the period of 1977–2017, the groundwater level decreased from the Gnangara’s edge to the central-north area, with a maximum trend magnitude of −0.28 m/year. The groundwater level in 1998–2017 exhibited an increasing trend in December–March and a decreasing trend in April–November with the exception of September when compared to 1978–1997. The rainfall + time model based on the cumulative annual residual rainfall technique with a one-month lag during 1990–2017 was determined as the best model. Rainfall had great impacts on the groundwater level in central Gnangara, with the highest impact coefficient being 0.00473, and the impacts reduced gradually from the central area to the boundary region. Other factors such as pine plantation, the topography and landforms, the Tamala Limestone formation, and aquifer groundwater abstraction also had important influences on the groundwater level.