The microporous mineral gaidonnayite Na 2 ZrSi 3 O 9 •2H 2 O was studied to better understand its ion-exchange mechanisms, specifically for Cs + and H + ions. In situ Raman spectroscopy, in situ X-ray diffraction (XRD), simultaneous thermogravimetric analysis and differential scanning calorimetry (TGA/DSC), and in situ X-ray fluorescence were used to determine the exchange processes involved. The Raman spectra contain strong peaks that can be attributed to the vibrational modes for the 3MR symmetric stretch at 500 cm −1 , Si−O−Zr−O chain stretches at 938 cm −1 , and Si−O stretching in the 1000−1100 cm −1 range. The most prominent Raman shift during ion exchange is found near the 520 cm −1 peak, which corresponds to distortions of the 3MR substructure of gaidonnayite. In all instances of this study, the 3MR exhibited the highest amount of distortion during ion exchange, and the evolution of this distortion is compared to unit-cell changes as measured from XRD data and elemental changes via XRF. The correlations between the Raman, XRD, and XRF data show rapid deformation of the 3MR during the onset of H + ion exchange in the Na form of gaidonnayite. Even when unit-cell volume changes were small (<3 Å 3 ) as in the cases for Cs + into Na-gaidonnayite and Cs + into H-gaidonnayite, significant changes in the ≈520 cm −1 peak were measured. By comparing XRD data and Raman data, and verifying the cation uptake by XRF, we were able to identify and confirm conformational changes and distortions in the crystal structure before, during, and after Cs + and H + exchange. Cs exchange occurred the fastest and with the greatest capacity when starting in the H-form at room temperature, and at elevated temperatures when starting in the Na-form.