Complex urban systems can be difficult to monitor, diagnose and manage because the complete states of such systems are only partially observable with sensors. State estimation techniques can be used to determine the underlying dynamic behavior of such complex systems with their highly non-linear processes and external time-variant influences. States can be estimated by clustering observed sensor readings. However, clustering performance degrades as the number of sensors and readings (i.e. feature dimension) increases. To address this problem, we propose a framework that learns a feature-centric lower dimensional representation of data for clustering to support analysis of system dynamics. We propose Unsupervised Feature Attention with Compact Representation (UFACR) to rank features contributing to a cluster assignment. These weighted features are then used to learn a reduced-dimension temporal representation of the data with a deep-learning model. The resulting low-dimensional representation can be effectively clustered into states. UFACR is evaluated on real-world and synthetic wastewater treatment plant data sets, and feature ranking outcomes were validated by Wastewater treatment domain experts. Our quantitative and qualitative experimental analyses demonstrate the effectiveness of UFACR for uncovering system dynamics in an automated and unsupervised manner to offer guidance to wastewater engineers to enhance industrial productivity and treatment efficiency.