The estimation of boundary layer losses requires the accurate specification of the freestream velocity, which is not straightforward in centrifugal compressor blade passages. This challenge stems from the jet-wake flow structure, where the freestream velocity between the blades cannot be clearly specified. In addition, the relative velocity decreases due to adverse pressure gradient. Therefore, the common assumption of a single freestream velocity over the blade surface might not be valid in centrifugal compressors. Generally in turbomachinery, the losses in the blade cascade boundary layers are estimated, e.g., with different loss coefficients, but they often rely on the assumption of a uniform flow field between the blades. To give guidelines for the estimation of the mentioned losses in highly distorted centrifugal compressor flow fields, this paper discusses the difficulties in the calculation of the boundary layer thickness in the compressor blade passages, compares different freestream velocity definitions, and demonstrates their effect on estimated boundary layer losses. Additionally, a hybrid method is proposed to overcome the challenges of defining a boundary layer in centrifugal compressors.