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Accurately predicting estuaries water quality is essential to support immediate intervention to water quality problem management. Deep learning is used to improve forecasting of water quality parameters in many aquatic systems. However, it is frequently constrained by low data frequency and quality. High-frequency, continuous monitoring using integrated in-situ water quality and environmental sensors can be an input to deep learning models resulting in highly accurate water quality and environmental predictions. This paper proposes a novel approach to improve forecasting of water quality and environmental variables. The results of the real-world data from the Swan Canning Estuary sites show how well the suggested model works. With different sizes of training and testing sets, the model can still predict the increased number of hours in high scores. Eliminating highly correlated variables impact the model's performance, emphasising the usefulness of strongly correlated variables in scarce data scenarios. • This article proposes a framework to enhance water quality variable forecasting. • The framework reframes the time series problem as a supervised learning problem. • The results on the set of data from the estuary show how well the framework works. • The approach is envisaged to support management in detecting water quality issues. [ABSTRACT FROM AUTHOR]