The stability of annealed proton exchange waveguides and devices in LiTaO3is examined by monitoring the output power ratio of passive directional couplers. This is shown to be an extremely sensitive technique for measuring waveguide stability. Mode propagation constants of planar waveguides and near‐field mode sizes and losses of channel waveguides are also measured as a function of time. Data from these measurements indicate that the refractive index profile is unstable and continuously evolves even for relatively long anneal times. The instabilities appear to lower the local change in the refractive index either through the room‐temperature migration of hydrogen or a change in the magnitude the refractive index increase due to the proton exchange. Assuming that the hydrogen concentration profile is stable, the decrease in the refractive index was estimated to be ≊10−3over a period of 90 days. Although the instabilities were seen in all of the fabricated devices, only a small portion of the total fabrication parameter space was investigated. Therefore, it is possible that the instability may be avoided as in LiNbO3, by using dilute melts or even longer anneal times.