In cold-climate regions, road salt is used as a deicer for winter road maintenance. The applied road salt melts ice and snow on roads and can be washed off through storm sewer systems into nearby urban streams, harming the freshwater ecosystem. Therefore, aiming to develop a precise and accurate model to determine future chloride concentration in the Credit River in Ontario, Canada, the present work makes use of a “Graph Neural Network”–“Sample and Aggregate” (GNN-SAGE). The proposed GNN-SAGE is compared to other models, including a Deep Neural Network-based transformer (DNN-Transformer) and a benchmarking persistence model for a 6 h forecasting horizon. The proposed GNN-SAGE surpassed both the benchmarking persistence model and the DNN-Transformer model, achieving RMSE and R2 values of 51.16 ppb and 0.88, respectively. Additionally, a SHAP analysis provides insight into the variables that influence the model’s forecasting, showing the impact of the spatiotemporal neighboring data from the network and the seasonality variables on the model’s result. The GNN-SAGE model shows potential for use in the real-time forecasting of water quality in urban streams, aiding in the development of regulatory policies to protect vulnerable freshwater ecosystems in urban areas.