We study a reduced order model (ROM) based waveform inversion method applied to a Helmholtz problem with impedance boundary conditions and variable refractive index. The first goal of this paper is to obtain relations that allow the reconstruction of the Galerkin projection of the continuous problem onto the space spanned by solutions of the Helmholtz equation. The second goal is to study the introduced nonlinear optimization method based on the ROM aimed to estimate the refractive index from reflection and transmission data. Finally we compare numerically our method to the conventional least squares inversion based on minimizing the distance between modelled to measured data.