The invention provides stable lithium niobate waveguides, and systems and methods for making same. In accordance with one aspect of the invention, a waveguide includes a lithium niobate substrate having an upper surface; and a soft proton-exchanged layer embedded within the substrate, the soft proton-exchanged layer formed by exposing the lithium niobate substrate to a proton exchange solution including a proton exchange acid and a lithium salt of the proton exchange acid at a temperature of less than an atmospheric boiling point of the solution, followed by annealing the lithium niobate substrate under a vapor pressure of water preselected to inhibit protons in the substrate from forming water and evaporating from the upper surface of the substrate. The preselected water vapor pressure may be between 0.1 atm and about 0.9 atm, for example, between about 0.4 atm and about 0.6 atm, in one embodiment about 0.47 atm.