Density functional theory-based thermodynamic modeling was performed to determine the effect of humidity and H2/O2 gas pressure on the defect chemistry and transport properties of proton conducting oxide BaZr1−xYxO3−δ (x ≤ 0.1) in the temperature range of 800–1200 K, relevant for solid oxide fuel/electrolysis cell applications. The first principles charge defect analysis was carried out to obtain the defect energetic ensembles as a function of Fermi level as well as the dependence of the hydration and oxidation reaction energies on complex defect-dopant configurations. It is shown that oxygen vacancies introduced to compensate for the extra Ba vacancies may cause a slight increase in the concentration of hydroxyl and proton species upon hydration of Ba deficient BaZr1−xYxO3−δ, while the overall proton diffusivity is predicted to decrease with increased proton hopping barriers upon trapping near the Ba vacancies. The developed defect model is further demonstrated to be able to describe the bulk defect chemistry and transport properties of BaZr0.9Y0.1O3−δ under the solid oxide cell operating conditions. The theoretical framework developed in this work further allows the inclusion of configurational, energetic and electronic characteristics of the defects that can be used as a complementary tool to experimental measurements for testing various mechanistic pathways or to provide essential mechanistic data.