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Apophyllite, a hydrous K-Ca-phyllosilicate, reacts with acidic aqueous solutions at room temperature. Various analytical methods have been applied to study the mechanism of the reaction and its characteristics, i.e. the changes in chemical composition, modifications in crystal structure and alterations in surface morphology. In contact with acidic solution, protonation of the terminal, non-bridging oxygen at the silicate tetrahedra takes place and the interlayer cations K+ and Ca2+ are removed. The protonation and ion removal causes the interlayer spacing to increase. Atomic force microscopy shows that the increase takes place discontinuously and, therefore, reflects a discontinuous reaction that comprises a two- or three-step protonation. Additionally, three structurally different protonation sites have been detected by nuclear magnetic resonance spectroscopy which also differ in the amount of close-by hydrogen, although in pristine apophyllite all terminal oxygen positions at silicate tetrahedra are structurally equivalent. In many clay minerals such structurally different protonation sites have not been detected so far. Thus, the multi-step protonation process in apophyllite clearly demonstrates the vast sensitivity of the protonation reaction on small structural variations in phyllosilicates.