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Contamination events in water distribution networks (WDN) pose significant threats to water supply and public health. Rapid and accurate contamination source identification (CSI) can facilitate the development of remedial measures to reduce impacts. Though many machine learning (ML) methods have been proposed for fast detection, there is a critical need for approaches capturing complex spatial dynamics in WDNs to enhance prediction accuracy. This study proposes a gated graph neural network (GGNN) for CSI in the WDN, incorporating both spatiotemporal water quality data and flow directionality between network nodes. Evaluated across various contamination scenarios, the GGNN demonstrates high prediction accuracy even with limited sensor coverage. Notably, directional connections significantly enhance the GGNN CSI accuracy, underscoring the importance of network topology and flow dynamics in ML-based WDN CSI approaches. Specifically, the method achieves a 92.27% accuracy in narrowing the contamination source to 5 points using just 2 h of sensor data. The GGNN showcases resilience under model and measurement uncertainties, reaffirming its potential for real-time implementation in practice. Moreover, our findings highlight the impact of sensor sampling frequency and measurement accuracy on CSI accuracy, offering practical insights for ML methods in water network applications. • A gated graph neural network is proposed for contamination source identification. • The new model utilizes network topology and flow directions for enhanced performance. • Improved sensor sampling frequency and measurement accuracy boost model performance. • Model exhibits resilience to demand and measurement uncertainties. [ABSTRACT FROM AUTHOR]