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The speciation and structure of Cu ions and complexes in chabazite (SSZ-13) zeolites, which are relevant catalysts for nitrogen oxide reduction and partial methane oxidation, depend on material composition and reaction environment. Ultraviolet-visible (UV-Vis) spectra of Cu-SSZ-13 zeolites synthesized to contain specific Cu site motifs, together with ab initio molecular dynamics and time-dependent density functional theory calculations, were used to test the ability to relate specific spectroscopic signatures to specific site motifs. Geometrically distinct arrangements of two framework Al atoms in six-membered rings are found to exchange Cu 2+ ions that become spectroscopically indistinguishable after accounting for the finite-temperature fluctuations of the Cu coordination environment. Nominally homogeneous single Al exchange sites are found to exchange a heterogeneous mixture of [CuOH] + monomers, O- and OH-bridged Cu dimers, and larger polynuclear complexes. The UV-Vis spectra of the latter are sensitive to framework Al proximity, to precise ligand environment, and to finite-temperature structural fluctuations, precluding the precise assignment of spectroscopic features to specific Cu structures. In all Cu-SSZ-13 samples, these dimers and larger complexes are reduced by CO to Cu + sites at 523 K, leaving behind isolated [CuOH] + sites with a characteristic spectroscopic identity. The various mononuclear and polynuclear Cu 2+ species are distinguishable by their different responses to reducing environments, with implications for their relevance to catalytic redox reactions.