Ionic liquid (IL)-catalyzed in situ transesterification (IST) of wet algae is a promising strategy for energy-efficient biodiesel production owing to the dual roles of ILs as both solvents of the cell wall and catalysts of transesterification, while their variations and interactions within different water contents, which subsequently affect biodiesel production, are still out of knowledge. Accordingly, the variations of fatty acid methyl ester (FAME) yields and cellulose solubilities of [Bmim][HSO4], [Bmim]- [H2PO4], and [Bmim]2[HPO4] under different water conditions are experimentally and theoretically studied. Results indicate that [Bmim][HSO4], [Bmim][H2PO4], and [Bmim]2[HPO4] are acid, weak alkaline, and strong alkaline catalysts of transesterification of lipid with methanol, respectively. FAME yields of both [Bmim]- [HSO4]- and [Bmim][H2PO4]-catalyzed reactions increase initially with the addition of 1.5 g of water, while they decrease with the increase of water content because of the consequent decline of the nucleophilic index and electrophilic index of the OH groups of [Bmim][HSO4] and [Bmim][H2PO4], respectively. Analogously, slight decreases of FAME yields of [Bmim]2[HPO4]-catalyzed transesterification are observed within 0.0−3.0 g of water, while a notable decrease is presented when 6.0 g of water is added. Contrary to the variation of catalytic properties, the cellulose solubilities of [Bmim][HSO4], [Bmim][H2PO4], and [Bmim]2[HPO4] all decrease with the addition of 1.5 g of water, as the water molecules occupy the H-bonding sites of [Bmim][HSO4]−cellobiose (clb), while the H-bonding interactions of water−clb and water− [Bmim][H2PO4] formed by shared oxygen atoms are enhanced with the increase of water content, subsequently enhancing the Hbonding interactions of ILs−clb and relative cellulose solubilities. The variations of cellulose solubilities of ILs with the addition of 0.0−6.0 g of water are opposite to those of their catalytic properties. This study indicates that the cellulose solubilities and catalytic properties of [Bmim][HSO4], [Bmim][H2PO4], and [Bmim]2[HPO4] compete with each other under different water conditions, providing a potential strategy to offset the negative effect of water content on IST of wet algae.