The influence of emission levels on the concentrations of four important air pollutants (ammonia, ozone, ammonium sulphate and ammonium nitrate) over three European cities (Milan, Manchester, and Edinburgh) with different geographical locations is considered. Sensitivity analysis of the output of the Unified Danish Eulerian Model according to emission levels is provided. The Sobol’ variance-based approach for global sensitivity analysis has been applied to compute the corresponding sensitivity measures. To measure the influence of the variation of emission levels over the pollutants concentrations the Sobol’ global sensitivity indices are estimated using efficient techniques for small sensitivity indices to avoid the effect of loss of accuracy. Theoretical studies, as well as, practical computations are performed in order to analyze efficiency of various variance reduction techniques for computing small indices. The importance of accurate estimation of small sensitivity indices is analyzed. It is shown that the correlated sampling technique for small sensitivity indices gives reliable results for the full set of indices. Its superior efficiency is studied in details.