Photoabsorber materials such as Cu2O, which are normally prone to degradation reactions in aqueous environment, have regained attention for photoelectrochemical water splitting (PEC) due to the use of protective overlayers. Furthermore, by implementing an additional interlayer between the photoabsorber and protective layer, the photovoltage and the overall device efficiency can be enhanced due to the increased built-in voltage at the p–n junction. The detailed analysis of these multilayer PEC photoelectrodes under operando conditions is challenging due to the multiplicity of interfaces and charge carrier processes. To facilitate routine investigation of such multilayer systems, we have established a resistance-based method using electrochemical impedance spectroscopy (EIS) to identify the underlying potential-dependent processes of water splitting photocathodes under operation, which quickly reveals the problematic interfaces in these structures. Cu2O/Ga2O3/TiO2/RuOx and p–Si/TiO2/RuOx photocathodes were investigated, with varying thicknesses of both interlayer and protection layer. The main limitations in the Cu2O devices were found to be the Ga2O3/TiO2 interface and the surface properties of the cuprous oxide absorber (most likely Cu2+ at the surface). We demonstrate that a commonly applied etching procedure of the Cu2O to remove surface impurities reduced the associated resistance, but was not sufficient to achieve an ideal interface to the electron accepting layer. The analysis scheme enabled us to shed light on most of the involved charge carrier processes taking place in these complex systems, and we expect that this method will be applicable to other multilayer systems, facilitating a more routine and powerful operando characterization method for water splitting photoelectrodes. Furthermore the knowledge gained in this investigation will pave the way for the development of a complete equivalent circuit model of these protected buried heterojunction photocathodes.