Fault or anomaly detection is one of the key problems faced by the chemical process industry for achieving safe and reliable operation. In this study, a novel methodology, spectral weighted graph autoencoder (SWGAE) is proposed, wherein, the problem of anomaly detection is addressed with the help of graphs. The proposed approach entails the following key steps. Firstly, constructing a spectral weighted graph, where each time step of a process variable in the multivariate time series dataset is modelled as a node in an appropriately tuned moving window. Subsequently, we propose to monitor the weights of the edges between two nodes that make a connection. The faulty instances are identified based on the discrepancy in the weight pattern compared to normal operating data. To this end, once the weights are determined, they are fed to the auto-encoder network, where reconstruction loss is calculated, and faults are identified if the reconstruction loss exceeds a threshold. Further, to make the proposed approach comprehensive, a fault isolation methodology is also proposed to identify the faulty nodes once the faulty variables are identified. The proposed approach is validated using Tennessee-Eastman benchmark data and pressurized heavy water nuclear reactor real-time plant data. The results indicate that the SWGAE method, when compared to the other state-of-the-art methods, yielded more accurate results in correctly detecting faulty nodes and isolating them.