In this study we present the role of the Planetary Boundary Layer Height (PBLH) on the air pollutant concentrations measured at an urban background station at the megacity of Athens, Greece, an area characterized by complex topography. For this purpose, we utilized in situ measurements of aerosol number concentrations at different size bins (10-200 nm) N10-200nm, (200-550 nm) N200-550nm, equivalent Black Carbon (eBC), and wind speed data, for the period of May - July 2020. According to our analysis, both horizontal transport and vertical mixing and dispersion of air pollutants play a critical role in air quality. More precisely, PBLH is negatively correlated with aerosol concentration. The increase in the height of the Planetary Boundary Layer (PBL) favors a reduction in aerosol concentration, which, to some extent, compensates for the increase in aerosol load due to emission sources and horizontal transport from the city center. The horizontal advection process is related to the PBLH, since a deep PBL drives the advection, while a shallow PBL is characterized by weak horizontal wind velocities. On the other hand, under stagnant air mass conditions, when the PBL shrinks, the concentrations of air pollutants increase. On average, a 25% increase in the PBLH results in a 15% reduction in aerosol concentration, whereas a 15% reduction in the PBLH may result in a 10% increase in aerosol concentrations. Overall, N10-200nm particle concentrations increases, when air masses arrive from the S-NW sector (city center) due to traffic and vehicle emissions, while transport of continental pollution mixed with local and regional emissions along the Balkans-Aegean Sea axis, is originating from the NE axis under high wind speeds. The latter is more clearly recognized from aged aerosol components such as sulphate. Whereas, the N200-550nm and eBC showed increased concentration load under stagnant air mass conditions, independently of the wind direction.