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Although traditional physical models have been used to analyse groundwater systems, the emergence of novel machine learning models can improve the accuracy of the predictions. Deep learning has been prominent in environmental and climate change problems. In this paper, we present a framework for utilising deep learning models to predict groundwater levels based on nearby streamflow and rainfall data. We address the missing data problem using a Bayesian linear regression model within the deep learning framework. Our deep learning framework utilises models such as long-short term memory (LSTM) networks and convolutional neural networks (CNN) for multi-step ahead time series prediction. We examine the fluctuations in groundwater levels at various boreholes located near Middle Creek in New South Wales, Australia. We use the National Collaborative Research Infrastructure Strategy (NCRIS) groundwater database and utilise Bayesian linear regression to impute missing data. We investigate the accuracy of the selected models for individual and regional basins and univariate and multivariate strategies. Our results show that the LSTM-based regional model with multivariate strategy using rainfall data provided the best accuracy. • We predict groundwater levels based on stream flow and rainfall data. • Our framework uses Bayesian data imputation and deep learning for multi-step prediction. • We examine the groundwater fluctuations at various boreholes located in Australia. • Results show a fine-tuned regional model with rainfall data yielded the best accuracy. • We find that LSTM models outperformed CNNs using the multivariate approach. [ABSTRACT FROM AUTHOR]