This research deals with consideration of the SPR sensor response in the framework of the scattering matrix approach with the modeling of biomolecular layer using Green’s function formalism and effective medium theories. It was found out that modeling of the SPR sensor response using abovementioned approaches in the densely packed monolayer approximation gave not enough agreement with the experiment. The reason was that real molecular layers are rarely densely packed. They usually can be characterized by molecular surface concentration or monolayer filling factor. Approximation of these parameters allows obtaining their values, which correspond to real biomolecular layers, and gives better agreement with the experiment.