The vertical aerosol layering of the troposphere is poorly documented in mountainous regions, particularly in the Alpine valleys, which are influenced by valley and mountain winds. To improve our knowledge of particulate matter trapped in the Annecy valley, synergetic measurements performed by a ground-based meteorological Raman lidar and a Rayleigh-Mie lidar aboard an ultralight aircraft were implemented as part of the Lacustrine-Water vApor Isotope inVentory Experiment (L-WAIVE) over Lake Annecy. These observations were complemented by satellite observations and Lagrangian modeling. The vertical profiles of aerosol optical properties (e.g., aerosol extinction coefficient (AEC), lidar ratio (LR), particle linear depolarization ratio (PDR)) are derived from lidar measurements at 355 nm during the period between 13 and 22 June 2019. The background aerosol content with an aerosol optical thickness (AOT) of 0.10 ± 0.05, corresponding to local–regional conditions influenced by anthropogenic pollution, has been characterized over the entirety of Lake Annecy thanks to the mobile ultralight payload. The aerosol optical properties are shown to be particularly variable over time in the atmospheric column, with mean LRs (PDRs) varying between 40 ± 8 and 115 ± 15 sr (2 ± 1 and 35 ± 2%). Those conditions can be disturbed by air masses that have recirculated over the valley, as well as by contributions from neighboring valleys. We have observed an important disruption in the atmospheric aerosol profiles by the arrival of an exceptionally dry air mass (RH ~ 30%), containing aerosols identified as coming from the Great Western Erg (AOT ~ 0.5, LR = 65 ± 10 sr, PDR = 20–35%) in the Sahara. These desert dust particles are shown to influence the entire atmospheric column in the Annecy valley. Such an experimental approach, coupling upward and downward lidar and spaceborne observation/Lagrangian modelling, was shown to be of significant interest for the long-term monitoring of the evolution of aerosol loads over deep valleys. It allows a better understanding of the influence of dust storms in the presence of severe convective weather processes.