A method for bonding a plurality of substrates includes performing a gas plasma treatment on the plurality of substrates, and performing a water plasma treatment on the plurality of substrates. Additionally, a system for performing low temperature plasma enhanced bonding includes a substrate housing structure having a substrate receiving volume, a gas source fluidly coupled to the substrate housing structure, a water vapor source fluidly coupled to the substrate housing structure, and a radio-frequency (RF) generator coupled to the substrate housing structure, wherein the system is configured to perform both a gas plasma treatment and a water plasma treatment on a substrate.