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There is great interest in the use of microfluidic paper-based analytical devices (μPADs) for low-cost diagnostics. In this contribution, we illustrate the utility of Raman spectral imaging for both μPAD characterization and for quantification of the transport of applied reagents and analytes within these devices. We evaluated the transport of nanoscale particles within μPADs using a suite of differentially functionalized gold (AuNP) and silver (AgNP) nanoparticles with diameters of 8-64 nm. Nanoparticle transport within the cellulose matrix was characterized by collection of both Raman and surface-enhanced Raman spectroscopy (SERS) spectral maps that enabled differentiation of cellulose fibers and characterization of analyte deposition patterns. The transport of citrate (cit), BSA, PEG, PVP, and DNA functionalized AuNP and AgNP in wax-printed μPADs was primarily affected by nanoparticle surface chemistry rather than particle size or core composition. Sample pH (3-10) influenced the transport of 15 nm BSA-cit-AuNP, but not 15 nm cit-AuNP, because of the effects of solution pH on the charge and conformation of BSA. Derjaguin, Landau, Verwey, and Overbeek theory (DLVO) and extended DLVO (xDLVO) theory are used to explain the collected experimental results.