Approaching single-crystal-like morphology has always been important in driving materials toward their optimal properties. With only orientational order, liquid crystal (LC) materials require dual-axis orientational control to optimize their structural order in the bulk phase. However, current external guiding fields such as electrical, magnetic, and mechanical guiding fields are less effective in aligning amphiphilic LCs. In this study, water is developed as an excellent structural stabilizer and orientation-directing agent of an amphiphilic discotic molecule (AD) in the water-induced self-assembly (WISA) process. Thermal analysis and structural characterization results show that water increases the stability and domain sizes of the hexagonal columnar (Colh) phase of the AD by co-assembling with the ADs to form bulk artificial water channels (AWCs). Moreover, through control over the nucleation conditions (degree of supercooling and location of nucleation), dual-axis alignment in both the planar and vertical growth of the AWCs is achieved by applying water as the guiding field in the directional WISA. With precise control over the hierarchical structures, the bulk AWC array of the AD delivers excellent salt rejection properties and water permeability. Considering that all the amphiphilic LCs have hydrophilic segments, these new roles of water in the WISA process could launch the further development of functional amphiphilic LCs by providing a dynamic interaction and a readily available guiding field.