Overhead road obstacles present a significant logistical hazard to the heavy vehicle industry. Traditional overheight vehicle warning systems such as passive warning systems (PWS) and active warning systems (AWS) have not adequately reduced the frequency and impact of overheight incidents, encouraging transportation agencies to employ intelligent transport system (ITS) strategies using state-of-the-art advanced technologies. This research takes an innovative approach in developing an immersive user-focused experience, harnessing multi-disciplinary methods and tools to engineer a spatial digital twin prototype for a novel Internet-of-Things (IoT)-based active warning alert and re-routing system (AWARS). LiDAR and 3D GIS were used to model the complex road environment, tailored to the strict fiscal objectives sought by economically mindful organisations. Tree crowns were extracted from near-Infrared aerial imagery and digital elevation models, supplying the dimensions necessary for 3D tree modelling. IoT connectivity was configured using a real-time analytics approach to deliver alerts and re-routing options. The World Traffic Service with live and predictive traffic data was used for the routing application programming interface (API). A standard-configuration common rigid truck (CRT) was inserted into the 3D road environment model to simulate overheight collisions and to ascertain the effect of re-routing on estimated time of arrival (ETA). Longer ETA durations were observed for routes computed by the digital twin. Theoretically, enhanced situational awareness and subsequent reduction of risk likelihood suggests an optimised response to industry demands, despite extended travel times, cultivating a favorable impact on the supply chain through enhanced safety management.