Hydrated niobium oxides are used as strong solid acids with a wide variety of catalytic applications, yet the correlations between structure and acidity remain unclear. New insights into the structural features giving rise to Lewis and Brønsted acid sites are presently achieved. It appears that Lewis acid sites can arise from lower coordinate NbO5 and in some cases NbO4 sites, which are due to the formation of oxygen vacancies in thin and flexible NbO6 systems. Such structural flexibility of Nb-O systems is particularly pronounced in high surface area nanostructured materials, including few-layer to monolayer or mesoporous Nb2O5·nH2O synthesized in the presence of stabilizers. Bulk materials on the other hand only possess a few acid sites due to lower surface areas and structural rigidity: small numbers of Brønsted acid sites on HNb3O8 arise from a protonic structure due to the water content, whereas no acid sites are detected for anhydrous crystalline H-Nb2O5.