This study investigated advancements in atmospheric forecasting by integrating real-time observational data into the Weather Research and Forecasting (WRF) model through the WRF-Data Assimilation (WRF-DA) framework. By refining atmospheric models, we aimed to improve regional high-resolution wave and hydrodynamic forecasts essential for environmental management. Focused on southern Greece, including Crete, the study applied a 3D-Var assimilation technique within WRF, downscaling forecasting data from the Global Forecast System (GFS) to resolutions of 9 km and 3 km. The results showed a 4.7% improvement in wind speed predictions, with significant gains during forecast hours 26–72, enhancing model accuracy across METAR validation locations. These results underscore the positive impact of the integration of additional observational data on model accuracy. This study also highlights the utility of refined atmospheric models for real-world applications through their use in forcing ocean circulation and wave models and subsequent Digital Twin of the Ocean applications. Two such applications—optimal ship routing to minimize CO2 emissions and oil spill trajectory forecasting to mitigate marine pollution—demonstrate the practical utility of improved models through what-if scenarios in easily deployable, containerized formats.