In the crystal structure of the title complex, [Zn(C3H2O4)(C12H8N2)(H2O)2], the Zn(II) atom displays a distorted octahedral geometry, being coordinated by two N atoms from the 1,10-phenanthroline ligand, two O atoms from different carboxylate groups of the chelating malonate dianion and two O atoms of cis water molecules. The complex molecules are linked to form a three-dimensional supramolecular array by both hydrogen-bonding interactions between coordinated water molecules and the uncoordinated carboxylate O atoms of neighboring molecules, and aromatic pi-pi stacking interactions between neighboring phenanthroline rings.