We present a comprehensive first-principles study of the ballistic transport properties of low-dimensional nanostructures such as linear chains of atoms (Al, C) and carbon nanotubes in the presence of defects. An approach is introduced where quantum conductance is computed from the combination of accurate plane-wave electronic structure calculations, the evaluation of the corresponding maximally localized Wannier functions, and the calculation of transport properties by a real-space Green's function method based on the Landauer formalism. This approach is computationally very efficient, can be straightforwardly implemented as a post-processing step in a standard electronic-structure calculation, and allows us to directly link the electronic transport properties of a device to the nature of the chemical bonds, providing insight onto the mechanisms that govern electron flow at the nanoscale.