SUMMARY We construct a 3-D shear-wave velocity model for the crustal structure and the geometry of the Adana and Iskenderun basins by using ambient noise tomography of Rayleigh waves. For this purpose, we compute interstation Green's functions and measure the group velocity dispersion in the period range of 8–25 s. Then Rayleigh wave group velocity maps obtained by tomographic inversion are used to derive a shear wave velocity model by linearized inversion. Both Rayleigh wave group velocity maps and the 3-D shear-wave velocity structure are correlated with the geology and the major tectonic features of the region. Cross sections taken from the velocity model suggest a sediment thickness of up to 11 km in the wedge-shaped Adana Basin with the velocity ranging between 2.4 and 2.9 km s−1. The horseshoe-like high velocities surrounding the basin correspond to the Taurus Mountains in the west and north, and the Amanos Mountains in the east. In the region, down to a depth of 35 km the crustal velocity varies between 2.9 and 3.7 km s−1. Our investigations reveal the detailed 3-D basin geometry and crustal structure that can be beneficial for hazard assessment, geodynamic modelling as well as hydrocarbon exploration studies.