Surface plasmon resonance (SPR) spectroscopy is an efficient probe of transient structural changes in molecular films. To analyze kinetic SPR data for such systems, generally it is necessary to adapt an adequate theoretical framework that would allow one to express the measured optical quantities (time-dependent shifts of the resonance angle or wavelength) in terms of the structural parameters (layer thickness, mass density, or surface coverage) of the sample molecules. We present here theoretical calculations and illustrative experimental results to address certain essential elements of this type of data analysis for transient SPR systems. The phenomenological framework we consider here is based on multilayer reflectivity calculations, and can be applied to a broad class of systems involving ordered molecular layers on supporting gold films. A typical application of these calculations is demonstrated through the analysis of specific SPR experiments designed to probe the kinetics of pH-induced structural changes in a molecular film of 11-mercaptoundecanoic acid (MUA) on a thin gold film.