In the title complex, [Zn(C₅H₉NO₇P₂)₂(H₂O)₂], the zinc atom is coordinated by two bidentate zoledronate [zoledronate = (2-(1-imidazole)-1-hydroxy-1,1′-ethylidenediphophonate)] ligands and two water molecules. The coordination number is 6. There is one half-molecule in the asymmetric unit with the zinc atom located on a crystallographic inversion centre. The anion exists as a zwitterion with an overall charge of -1; the protonated nitrogen in the ring has a positive charge and the two phosphonates groups each have a single negative charge. There are two intramolecular O–H⋯O hydrogen bonds. The molecules are linked into a chain by intermolecular O–H⋯O hydrogen bonds. Adjacent chains are further linked by O–H⋯O hydrogen bonds involving the aqua ligands. An N–H⋯O interaction is also observed.