Heterpolyacids (HPAs) demonstrate catalytic activity for oxidative and acid-catalyzed hydrocarbon conversion processes. Deactivation and thermal instability, however, have prevented their widespread use. Herein, ab initio density functional theory is used to study the thermal decomposition of the Keggin molecular HPA structure through the desorption of constitutional water molecules. The overall reaction energy and activation barrier are computed for the overall reaction HnXM12O40 → H n-2XM12O39 + H2O. and subsequently used to predict the effect of HPA composition on thermal stability. For example, the desorption of a constitutional water molecule is found to be increasingly endothermic in the order silicomolybdic acid (H4SiMo 12O40) < phosphomolybdic acid (H3PMo 12O40) < silicotungstic acid (H4SiW 12O40) < phosphotungstic acid (H3PW 12O40), in agreement with the experimental ordering of their thermal stability. The presence of an adjacent Keggin unit may stabilize the structural defect created by the water desorption, thus suggesting that constitutional water loss is an initial step toward the decomposition into a bulk mixed oxide. The equilibrium concentration of defective Keggin units is determined as a function of temperature and water partial pressure. It is concluded that the loss of constitutional water molecules is a plausible deactivation mechanism of the acid catalyst. The intermediate structures along the decomposition path are proposed as possible active sites for oxidation catalysis. The results presented herein provide molecular level insight into the dynamic nature of the heteropolyacid catalyst structure.