While there is substantial evidence proving the success of transdermal drug delivery, there have been few accomplishments in the area of depth-resolved prediction of drug concentration during diffusion through a matrix. Such a method for noninvasive quantification of a diffusing species could assist in the development of new drugs, dosage forms, and penetration enhancers. Near-infrared depth-resolved measurements were accomplished by strategically controlling the amount of reflected light reaching the detectors using a combination of diaphragms with different-diameter apertures. Near-IR spectra were collected from a set of cellulose and Silastic® membranes to prove the possibility of depth-resolved near-IR measurements. Principal component regression was used to estimate the depth resolution of this method, yielding an average resolution of 31 μm. Further, to demonstrate depth-resolved near-IR spectroscopy in a practical <i>in vitro</i> system, we determined concentrations of salicylic acid (SA) in a hydrogel matrix during diffusion experiments carried out for up to three hours. An artificial-neural-network-based calibration model was developed which predicted SA concentrations accurately (<i>R</i><sup>2</sup> = 0.993, SEP = 123 μg/mL).

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