Abstract: Anderson's theorem states that non-magnetic impurities do not change the bulk properties of conventional superconductors. However, as the dimensionality is reduced, the effect of impurities becomes more significant. Here we investigate superconducting nanowires with diameter comparable to the Fermi wavelength $\lambda_F$ (which is less than the superconducting coherence length) by using a microscopic description based on the Bogoliubov-de Gennes method. We find that: 1) impurities strongly affect the superconducting properties, 2) the effect is impurity position dependent, and 3) it exhibits opposite behavior for resonant and off-resonant wire widths. We show that this is due to the interplay between the shape resonances of the order parameter and the subband energy spectrum induced by the lateral quantum confinement. These effects can be used to manipulate the Josephson current, filter electrons by subband and investigate the symmetries of the superconducting subband gaps.