The structure of the title compound [(ammine)(aqua)(2,6-dimethylphenyliminodiacetato-N,O,O '')copper(II)] consists of discrete neutral [CU(C12H13NO4)(H2O>(NH3)] molecules. The Cu atom is five-coordinate, with four short bonds formed with the N atom and two O atoms of the doubly deprotonated ligand and the N atom of the ammonia molecule. The water molecule is coordinated in an axial position at a longer distance. The coordination polyhedron can be described as a square-based pyramid with a small trigonal-bipyramidal distortion.