The crystal structure of clinoatacamite, ideally Cu2(OH)3Cl, has been studied using single-crystal X-ray diffraction and Raman scattering at variable temperature between 150 and 490 K in natural samples with different degrees of Co and Ni substitution. The monoclinic clinoatacamite crystal structure is closely related to the trigonal crystal structures of herbertsmithite, Cu3Zn(OH)6Cl2, and paratacamite, Cu3(Cu, Zn)(OH)6Cl2. Disappearance of clinoatacamite superstructure reflections close to a temperature of 400 K indicates the transition to a trigonal herbertsmithite-type phase in all crystals containing Co and Ni impurities. In these crystals, which are invariably twinned at room temperature, an intermediate phase is observed in the temperature range 360–400 K, which has the trigonal paratacamite crystal structure. Untwinned end-member clinoatacamite directly transforms to the herbertsmithite-type at T c = 445 K. Probability density functions of the oxygen and copper atoms as well as details from the Raman scattering measurements indicate that the interlayer Cu-coordination environment remains locally Jahn–Teller-distorted in the trigonal crystal structures with space group symmetries R3¯¯¯ and R3¯¯¯m and that the transition from monoclinic to trigonal symmetry is driven by the dynamic Jahn–Teller effect.