Atomistic computer modelling techniques are used to investigate the substitution of dopants in the CaZrO3 perovskite and the incorporation of protons in the Ba2In2O5 brownmillerite. The defect calculations on CaZrO3 predict that small trivalent cations show Zr-site selectivity with oxygen vacancy compensation, while larger cations show Ca-site selectivity with Ca vacancy compensation. EXAFS experiments on doped CaZrO3 demonstrate Yb and Nd substitution at Zr and Ca sites, respectively, in agreement with the simulations. Finally, several water incorporation reactions in Ba2In2O5 have been examined, including mechanisms involving oxygen interstitial sites.