Hydrogels have emerged as prototypical stimuli‐responsive materials with potential applications in soft robotics, microfluidics, tissue engineering, and adaptive optics. To leverage the full potential of these materials, fabrication techniques capable of simultaneous control of microstructure, device architecture, and interfacial stability, that is, adhesion of hydrogel components to support substrates, are needed. A universal strategy for the microfabrication of hydrogel‐based devices with robust substrate adhesion amenable to use in liquid environments would enable numerous applications. This manuscript reports a general approach for the facile production of covalently attached, ordered arrays of microscale hydrogels (microgels) on silicone supports. Specifically, silicone‐based templates are used to: i) drive mechanical assembly of prepolymer droplets into well‐defined geometries and morphologies, and ii) present appropriate conjugation moieties to fix gels in place during photoinitiated crosslinking via a “graft from” polymerization scheme. Automated processing enabled rapid microgel array production for characterization, testing, and application. Furthermore, the stimuli‐responsive microlensing properties of these arrays, via contractile modulated refractive index, are demonstrated. This process is directly applicable to the fabrication of adaptive optofluidic systems and can be further applied to advanced functional systems such as soft actuators and robotics, and 3D cell culture technologies.