Integrated optics provides an ideal test bed for the emulation of quantum systems via continuous-time quantum walks. Here we study the evolution of two-photon states in an elliptic array of waveguides. We characterise the photonic chip via coherent-light tomography and use the results to predict distinct differences between temporally indistinguishable and distinguishable two-photon inputs which we then compare with experimental observations. Our work highlights the feasibility for emulation of coherent quantum phenomena in three-dimensional waveguide structures.