Water reorientation is essential in a wide range of chemical and biological processes. However, the effects of such reorientation through rotation around the metal-oxygen bond on the chemical and physical properties of the resulting complex are usually ignored. Most studies focus on the donor property of water as a recognized σ donor-type ligand rather than a participant in the π interaction. Although a theoretical approach to study water-rotation effects on the functionality of a complex has recently been conducted, it has not been experimentally demonstrated. In this study, we determine that the magnetic anisotropy of a Co(II) complex can be effectively controlled by the slight rotation of coordinating water ligands, which is achieved by a two-step structural phase transition. When the water molecule is rotated by 21.2 ± 0.2° around the Co-O bond, the directional magnetic susceptibility of the single crystal changes by approximately 30% along the a-axis due to the rotation of the magnetic anisotropy axis through the modification of the π interaction between cobalt(II) and the water ligand. The theoretical calculations further support the hypothesis that the reorientation of water molecules is a key factor contributing to the magnetic anisotropy transition of this complex.