Patterned hydrogels of glycerol monomethacrylate (GMM)-co-acrylic acid (AA) were prepared in microchannels using an in situ photopolymerization method. Oxidation of the hydrogel was accomplished using aqueous sodium periodate (NaIO4) to produce an aldehyde functionalized surface. The depth of oxidation, characterized by confocal microscopy after conjugation with a fluorescent dye, was controlled by varying the NaIO4 concentration, reaction time, and temperature. Hydrogel oxidation was modeled by combining the Nernst-Planck, Poisson, Arrhenius, and rate equations. The modeling studies suggest that the glycol oxidation reaction and the diffusion of oxidant into the hydrogel are competitive factors in determining the oxidation depth. Once modified, these hydrogels have the ability to covalently bind small molecules and biomolecules to their surface under mild, aqueous conditions. For example, fluorescently labeled bovine serum albumin (FITC-BSA) was site-specifically conjugated to the surface of a photopatterned hydrogel via reductive amination.