Abstract: The Internet of Things (IoT) has revolutionized the functionality and efficiency of distributed cyber-physical systems, such as city-wide water treatment systems. However, the increased connectivity also exposes these systems to cybersecurity threats. This research presents a novel approach for securing the Secure Water Treatment (SWaT) dataset using a 1D Convolutional Neural Network (CNN) model enhanced with a Gated Recurrent Unit (GRU). The proposed method outperforms existing methods by achieving 99.68% accuracy and an F1 score of 98.69%. Additionally, the paper explores dimensionality reduction methods, including Autoencoders, Generalized Eigenvalue Decomposition (GED), and Principal Component Analysis (PCA). The research findings highlight the importance of balancing dimensionality reduction with the need for accurate intrusion detection. It is found that PCA provided better performance compared to the other techniques, as reducing the input dimension by 90.2% resulted in only a 2.8% and 2.6% decrease in the accuracy and F1 score, respectively. This study contributes to the field by addressing the critical need for robust cybersecurity measures in IoT-enabled water treatment systems, while also considering the practical trade-off between dimensionality reduction and intrusion detection accuracy.