A hydrated natural Ca-chabazite, (Ca1.86Na0.13K0.09)(Al3.98Si8.03)O24·12.38H2O, and its Cs-exchanged form, (Cs2.66Ca0.45Na0.04K0.10)(Al4.04Si8.04)O24·8.52H2O, have been studied by the structure analyses based on single-crystal X-ray diffraction data. In the hydrated natural Ca-chabazite, all of extraframework species were found at the essentially identical locations to those in previously reported room-temperature structure. On the other hand, we revealed that the Cs-exchanged form has the essentially ten occupied-sites in extraframework: four water sites (OW2′, OW3, OW4, OW5), essentially two Cs sites (Cs1/Cs1′, Cs2) and four Ca sites (Ca1, Ca2, Ca3, Ca4). The Cs+ ions more preferentially occupy the Cs1/Cs1′ site, located at/around the centers of the 8-membered ring windows of [4126286]-cavities, than the Cs2 site. The Cs1/Cs1’ and Cs2 sites are essentially identical to the OW2 and OW3 sites observed in the hydrated natural Ca-chabazite, respectively; thus, these Cs sites are produced by replacing water molecules in both OW sites with Cs+ ions. In terms of interatomic distances, the coordination environments of the extraframework species in the chabazite crystals before and after the Cs-exchange treatment are discussed. In particular, both samples have a common feature that possible hydrogen bonds are relatively weak between water molecules and framework O atoms, whereas those are relatively strong between water molecules. On the basis of the present findings, we discuss the crystal-chemical key factors for an excellent Cs-exchange ability of chabazite as a highly efficient radioactive-element remover.