Aerosol vertical profiles are valuable inputs for the evaluation of aerosol transport models, in order to improve the understanding of aerosol pollution ventilation processes which drive the dispersion of pollutants in mountainous regions. With the aim of providing high-accuracy vertical distributions of particle mass concentration for the study of aerosol dispersion in small-scale valleys, vertical profiles of aerosol mass concentration for aerosols from different sources (including Saharan dust and local biomass burning events) were investigated over the Vipava valley, Slovenia, a representative hot-spot for complex mixtures of different aerosol types of both anthropogenic and natural origin. The analysis was based on datasets taken between 1–30 April 2016. In-situ measurements of aerosol size, absorption, and mass concentration were combined with lidar remote sensing, where vertical profiles of aerosol concentration were retrieved. Aerosol samples were characterized by SEM-EDX, to obtain aerosol morphology and chemical composition. Two cases with expected dominant presence of different specific aerosol types (mineral dust and biomass-burning aerosols) show significantly different aerosol properties and distributions within the valley. In the mineral dust case, we observed a decrease of the elevated aerosol layer height and subsequent spreading of mineral dust within the valley, while in the biomass-burning case we observed the lifting of aerosols above the planetary boundary layer (PBL). All uncertainties of size and assumed optical properties, combined, amount to the total uncertainty of aerosol mass concentrations below 30% within the valley. We have also identified the most indicative in-situ parameters for identification of aerosol type.