In this paper, surface-activation-based nanobonding technology and its applications are described. This bonding technology allows for the integration of electronic, photonic, fluidic and mechanical components into small form-factor systems for emerging sensing and imaging applications in health and environmental sciences. Here, we describe four different nanobonding techniques that have been used for the integration of various substrates — silicon, gallium arsenide, glass, and gold. We use these substrates to create electronic (silicon), photonic (silicon and gallium arsenide), microelectromechanical (glass and silicon), and fluidic (silicon and glass) components for biosensing and bioimaging systems being developed. Our nanobonding technologies provide void-free, strong, and nanometer scale bonding at room temperature or at low temperatures (<200 °C), and do not require chemicals, adhesives, or high external pressure. The interfaces of the nanobonded materials in ultra-high vacuum and in air correspond to covalent bonds, and hydrogen or hydroxyl bonds, respectively.