This paper considers an indirect measurement approach to reconstruct a defect in a two-dimensional waveguide model for a non-destructive ultrasonic inspection via derivative-based optimization. The propagation of the mechanical waves is simulated by the scaled boundary finite element method that builds on a semi-analytical approach. The simulated data are then fitted to given data associated with the reflected waves from a defect which is to be reconstructed. For this purpose, we apply an iteratively regularized Gauss-Newton method in combination with algorithmic differentiation to provide the required derivative information accurately and efficiently. We present numerical results for three kinds of defects, namely, a crack, delamination, and corrosion. The objective function and the properties of the reconstruction method are investigated. The examples show that the parameterization of the defect can be reconstructed efficiently as well as robustly in the presence of noise.