Wavelet transform (WT) has been proven to be a powerful chemometric method for processing analytical data. In this review, works on the application of WT in processing near-infrared (NIR) spectrum were summarized, emphasizing the structural analysis of water in aqueous systems. The spectral features of water can be obtained from the resolution-enhanced NIR spectrum with the help of WT. Taking advantage of WT in resolution enhancement and the sensitivity of NIR spectroscopy for water, the spectral features for different water structures can be obtained, which makes water to be a potential NIR spectroscopic probe to detect the structural information of water and analyte in aqueous systems. Using the spectral variation of water with temperature, the interaction of water and solutes, and the role of water in chemical and bio-processes, such as the aggregation of proteins and polymers, was demonstrated. The spectral changes of the NIR spectrum with temperature were found able to reflect the structural changes of biomolecules or polymers in the analyzing systems.