The defect concentration in the prototypical metal-organic framework UiO-66 can be well controlled during synthesis, leading to precisely tunable physicochemical properties for this structure. However, there has been a long-standing debate regarding the nature of the compensating species present at the defective sites. Here, we present unambiguous spectroscopic evidence that the missing-linker defect sites in an ambient environment are compensated with both carboxylate and water (bound through intermolecular hydrogen bonding), which is further supported by ab initio calculations. In contrast to the prevailing assumption that the monocarboxylate groups (COO-) of the modulators form bidentate bonding with two Zr4+ sites, COO- is found to coordinate to an open Zr4+ site in an unidentate mode. The neighboring Zr4+ site is terminated by a coordinating H2O molecule, which helps to stabilize the COO- group. This finding not only provides a new understanding of defect termination in UiO-66, but also sheds light on the origin of its catalytic activity.