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H₂O molecules in emerald channels have been extensively discussed over the past half century. Recent studies paid attention to their classification and coordination, but have mostly focused on the type related to Na⁺. There are few works on the other types, and the related infrared (IR) absorption bands are rather controversial. This paper investigated natural emeralds from China and Colombia by means of micro-Fourier transform infrared (μ-FTIR) spectroscopy, micro-confocal Raman spectroscopy, and laser ablation-inductively coupled plasma mass spectrometry (LA-ICP-MS). The results suggested that doubly (IId) and singly (IIs) coordinated H₂O molecules were incorporated in natural emerald channels. Type IId H₂O predominated in those emeralds with relatively low alkali content. As the alkali content increased, the proportion of type IIs H₂O rose, stemming from the decrease of the H₂O^II/Na⁺ apfu ratio. Moreover, IR bands of H₂O corresponding to Li⁺ and Cs⁺ were tentatively ascribed here. IR bands for D₂O and HDO in Colombian sample were observed in the range of 2600–2850 cm⁻¹ and preliminarily assigned, which might be a potential tool for emerald origin determination. Our work expanded the existing classification of water molecules in emerald channels and redefined the controversial IR absorption bands.