Given the large surface area-to-volume ratios commonly encountered in microfluidics applications, the ability to engineer the chemical properties of surfaces encountered in these applications is critically important. However, as various polymers are rapidly replacing glass and silicon as the chosen materials for microfluidics devices, the ability to easily modify the surface chemistry has been diminished by the relatively inert nature of some commonly employed polymer surfaces, such as poly(methyl methacrylate) (PMMA), polystyrene, and polydimethylsiloxane (PDMS). This paper describes the low-temperature, vapor-phase deposition of robust silica layers to PMMA, polystyrene, and PDMS surfaces, which enables the functionalization of these surfaces by standard organosilane chemistries. Attenuated total reflection infrared spectroscopy, contact angle goniometry, ellipsometry, and atomic force microscopy are used to characterize the silica layers that form on these surfaces. Aqueous immersion experiments indicate that the silica layer has excellent stability in aqueous environments, which is a prerequisite for microfluidics applications, but for PMMA surfaces, low adhesion of the silica layer to the underlying substrate is problematic. For PDMS substrates, the presence of the silica layer helps to slow the process of hydrophobic recovery, which is an additional advantage.