Multimode optical interferometers represent the most viable platforms for the successful implementation of several quantum information schemes that take advantage of optical processing. Examples range from quantum communication and sensing, to computation, including optical neural networks, optical reservoir computing, or simulation of complex physical systems. The realization of such routines requires high levels of control and tunability of the parameters that define the operations carried out by the device. This requirement becomes particularly crucial in light of recent technological improvements in integrated photonic technologies, which enable the implementation of progressively larger circuits embedding a considerable amount of tunable parameters. We formulate efficient procedures for the characterization of optical circuits in the presence of imperfections that typically occur in physical experiments, such as unbalanced losses and phase instabilities in the input and output collection stages. The algorithm aims at reconstructing the transfer matrix that represents the optical interferometer without making any strong assumptions about its internal structure and encoding. We show the viability of this approach in an experimentally relevant scenario, defined by a tunable integrated photonic circuit, and we demonstrate the effectiveness and robustness of our method. Our findings can find application in a wide range of optical setups, based on both bulk and integrated configurations.