Alpine valleys are sensitive to anthropogenic emissions. Local atmospheric dynamics are a key factor that may lead to an accumulation of pollutants in the bottom of the Chamonix and Maurienne valleys. Assessment of 2010 pollutant concentrations variability needs to take these specificities into account. A meteorological data classification is combined with different emission scenarios in order to run an air quality model. Using simulations of representative scenarios rather than complete years allows for a fine spatial and temporal representation of local atmospheric dynamics and gives access to detailed chemical breakdowns. Results demonstrate the variability of primary and secondary species due to emissions and the predominance of local effects on pollutant concentrations.