We study the polarization properties of elliptical femtosecond-laser-written waveguide arrays. An analytical model is presented to explain the asymmetry of the spatial transverse profiles of linearly polarized modes in these waveguides. This asymmetry produces a polarization-dependent coupling coefficient, between adjacent waveguides, which strongly affects the propagation of light in a lattice. Our analysis explains how this effect can be exploited to tune the final intensity distribution of light propagated through the array and links the properties of a polarizing beam splitter in integrated optical circuits to the geometry of the waveguides.