Environmental unhealthiness has drastically increased global morbidity rates. In the Aburrá Valley (Medellín), this issue is exacerbated by accelerated urban development and a complex topography that hinders the transport and dispersion of pollutants toward less populated areas. Current monitoring networks, primarily concentrated in low-altitude zones, present limitations in providing data on pollutant behavior within densely populated slopes. This research addresses this scientific gap through mathematical modeling and computational simulation of particulate matter (PM) and gases COS, NOX) originating from mobile, fixed, and forest fire sources. 2D and 3D models were developed, incorporating the system's complex topography and characterizing flow and environmental conditions. Computational simulations were implemented by analyzing flow model behavior on morphologically complex meshes using the Finite Element Method (FEM) and particle dynamics. The model integrates drag dynamics and Brownian motion to simulate the transport and localized deposition of micro-particles. Results demonstrated that the valley's morphology acts as a physical barrier, creating stagnation zones on the slopes where wind velocity decreases by approximately 40%. Findings indicate that PM2.5 concentrations in these areas—which have lacked monitoring strategies—are over 30% higher during critical episodes. The study concludes that topography and urban density orient and retain pollutants, representing an elevated risk for vulnerable populations, especially in high-altitude zones. These findings provide robust technical support for regional authorities to optimize urban planning and environmental health regulations in the most critical urban areas of the Aburrá Valley.