Feasibility of nuclear magnetic resonance (nMR) was tested for research of anatomy and moisture content of wood. A three m high living beech tree (Fagus sylvatica L.) was imaged by magnetic resonance using the 3D spin-echo microscopic imaging technique at isotropic spatial resolution of 100 mm to follow structural changes in the topped branch caused by healing response mechanisms of the tree. Conventional light microscopy was also employed to verify tree structures detected on MR images. Conventional light microscopy revealed anatomical structures and three year age of the tree branch. MR images clearly showed pith, radially oriented xylem rays, early wood vessels with a delineated border between early and late wood, as well as the cambial zone with current xylem and phloem growth increment. We studied water concentration in the branch and the depth of dehydration formed in 22 hours after the mechanical injury. The dehydrated region extended to the mm depth from the wound location. First passive response of the injured branch tissue reflects in the initial decrease of the moisture content that was detected by MR imaging. Finally, we processed 3D MR microscopy data by the ImageJ image processing program to depict the spatial water concentration in the tree branch and to determine tissues with high water content.