Acceptor-doped LaNbO4 is a promising electrolyte material for proton-conducting fuel cell (PCFC) applications. As charge transfer processes govern device performance, the outermost surface of acceptor-doped LaNbO4 will play an important role in determining the overall cell performance. However, the surface composition is poorly characterized, and the understanding of its impact on the proton exchange process is rudimentary. In this work, the surface chemistry of 1 atom % Sr-doped LaNbO4 (La0.99Sr0.01NbO4-d, denoted as LSNO) proton conductor is characterized using LEIS and SIMS. The implication of a surface layer on proton transport is studied using the isotopic exchange technique. It has shown that a Sr-enriched but La-deficient surface layer of about 6–7 nm thick forms after annealing the sample under static air at 1000 °C for 10 h. The onset of segregation is found to be between 600 and 800 °C, and an equilibrium surface layer forms after 10 h annealing. A phase separation mechanism, due to the low solubility of Sr in LaNbO4, has been proposed to explain the observed segregation behavior. The surface layer was concluded to impede the water incorporation process, leading to a reduced isotopic fraction after the D216O wet exchange process, highlighting the impact of surface chemistry on the proton exchange process.