Hydrogels formed from (meth)acrylated poly(ethylene glycol) precursors are commonly used in a variety of biomedical applications ranging from tissue engineering to biosensors. While this approach has proven quite diverse, a major limitation to this approach is the heterogeneities and nonidealities that arise in the gels from the chain polymerization process, which increases the difficulty in relating the network structure to the final physical properties of the gel. Here we have exploited the specificity and fidelity of the [3+2] cycloaddition reaction to synthesize hydrogels with controlled architectures and improved mechanical properties. Moreover, we demonstrate a general approach toward the integration of multifunctional photoreactive polypeptide sequences into the network structure that provides a facile way to independently tune the 3D chemical and physical properties of the gel. Standard photolithographic techniques were used to generate a variety of two- and three-dimensional patterns as well as controlled biochemical gradients within existing preformed hydrogels.