The dependence of H-1 and C-13 NMR chemical shifts of 1-butyl-3-methylimidazolium ([bmim])-based room-temperature ionic liquids on the counteranion ([BF4], [MeSO4]) is investigated experimentally and computationally. The local structure of the ionic liquids is investigated by means of DFT calculations of the structure of ion pairs and molecular dynamics simulations. Clusters extracted from the simulation runs are used to calculate H-1 and C-13 chemical shifts by means of QM/MM methods with various partition schemes. Proton H2 of the imidazolium ring is the most sensitive to the counteranion; its chemical shift is strongly dependent on subtle details of the arrangement of the two closest anions. It is shown that a correct spacing of signals can be attained by including the two anions closest to C2 and H2 in the QM layer.