This study investigates the hydrodynamic and environmental behavior of Polyfytos Lake in Greece using the three-dimensional modeling tools developed in Delft for water and environmental systems (Delft3D), including the particle tracking module (Delft3D-PART) for simulating the transport and dispersion of pollutants. The primary objective was to simulate water movement and assess the dispersion of a hypothetical pollutant, such as oil, under realistic atmospheric conditions. Meteorological forcing was provided by high-resolution data derived from the Weather Research and Forecasting (WRF) model, ensuring an accurate representation of wind, temperature, and precipitation patterns across the lake surface. The integration of WRF data into Delft3D enabled dynamic and time-dependent boundary conditions that significantly enhanced the reliability of the simulation. A hypothetical heavy oil spill was introduced, with specific properties designed to emulate the behavior and transport of an oil-like substance. The Delft3D-PART module was employed to model the particle-based transport of the pollutant, tracking its movement, dispersion, and interactions with the lake’s hydrodynamic conditions over time. Its distribution was monitored to evaluate potential environmental impacts and inform response strategies. The study demonstrates the utility of Delft3D as a decision-support tool for environmental risk assessment and highlights the importance of incorporating realistic meteorological forcing into hydrodynamic models for effective management of complex inland water bodies.