Aggregated states of celluloses remain poorly understood, and therefore, the topic requires careful investigation. In this study, Raman, IR, and X-ray diffraction (XRDs) were used to study cotton microcrystalline cellulose (MCC) and MCC that has been ball-milled to various degrees. Raman and IR spectroscopy methods indicated that when these ball-milled samples were wet with water, most underwent conformational changes at the molecular level. Although formation of cellulose II was observed in longer duration ball-milled samples, the changes primarily gave rise to increased contributions in spectral and diffraction regions typically associated with the contributions of crystalline cellulose I. Moreover, when the wet samples were air-dried at 25 °C, the newly formed cellulose I-like structures partly reverted to the previous form present in the initial dry state. These findings explained for the previously reported XRD and NMR observations, where the addition of water resulted in increased crystallinities of cellulose samples. The implications of these findings to cellulose crystallinity measurements and other situations are discussed.