This study describes the atmospheric aerosol load encountered over a number of sites from the Southern Balkan region with a relatively well-known air quality factor. Using the aerosol optical depth AOD, retrieved from the two Moderate Resolution Imaging Spectroradiometers, MODIS, on board the Terra and Aqua NASA satellites, the aerosol content of numerous sites is investigated under the scope of local pollution sources, inter-regional transport and large scale dust and/or biomass burning events. The wide time range of seven full years of MODIS/Terra measurements permits the discussion of possible climatological aspects as well. The MODIS AOD is further validated using ground-based Brewer spectrophotometer measurements over a metropolis of Northern Greece, Thessaloniki. Thessaloniki is situated in a unique sea-side location which inflicts it with high humidity and sea-salt particles, and is furthermore frequently affected by biomass burning and desert dust aerosols arriving from surrounding sources. Local and regional pollution further influences the quality of the local air and the observed tropospheric optical depth. The air masses responsible for either transporting polluted air into the free troposphere or circulating boundary layer aerosol load around the region of Norther Greece have been identified and discussed in detail.