Microfluidic and nanofluidic systems are dominated by fluid-wall interactions due to enormous surface-area-to-volume ratios in these devices. Therefore, strategies to control wall properties in a reliable and repeatable manner can be important for device operation. Chemical modification of surfaces provides one such method. However, the stability of the surface adhered layers under fabrication and likely device operating conditions have not been evaluated in depth. This paper presents the stability analysis of three surface layers used in the 'click' chemistry methodology for surface modification. The three surface layers have bromo, amine, and methyl termination on glass surfaces. All three surface groups are exposed to various wet and dry conditions including acid, base, solvent, electrolyte buffer solutions, oxidative plasmas, UV light, and thermal processing conditions. Contact angle measurements, X-ray photoelectron spectroscopy, and atomic force microscopy were used to quantify the stability of the adhered surface layers. The data show that the brominated surface was stable to most test conditions, while both the amine and methyl surface layers were stable to a narrower set of test conditions.