As the largest freshwater storage in the world, groundwater plays an important role in maintaining ecosystems and helping humans adapt to climate change. However, groundwater dynamics, such as groundwater recharge, cannot be measured directly and is influenced by spatially and temporally complex processes, models are therefore required to capture the dynamics and provide scientific advice for decision-making. This paper developed, estimated and compared the performance of linear regression, multi-layer perception (MLP) and Long Short-Term Memory (LSTM) models in predicting groundwater recharge. The experimental dataset consists of time series of annual recharge from the year 1970 to 2012, based on water table fluctuation estimates from 465 bores in the states of South Australia and Victoria, Australia. We identified the factors that influenced groundwater recharge and found that the correlation between rainfall and groundwater recharge was strongest. The linear regression model had the poorest fitting performance, with the root mean squared error (RMSE) being greater than 0.19 when various proportions of training data were considered. The MLP model outperformed the linear regression in the prediction capability, achieving RMSE = 0.11 when 80% of training data was considered. The LSTM model was found to have the best performance, whose root mean squared errors were less than 0.12 when various proportions of training data were applied. The relative importance of influential predictors was evaluated using the above three models.