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Metal-organic frameworks (MOFs) constructed from Zr6-based nodes have recently received considerable attention given their exceptional thermal, chemical, and mechanical stability. Because of this, the structural diversity of Zr6-based MOFs has expanded considerably and in turn given rise to difficulty in their precise characterization. In particular it has been difficult to assign where protons (needed for charge balance) reside on some Zr6-based nodes. Elucidating the precise proton topologies in Zr6-based MOFs will have wide ranging implications in defining their chemical reactivity, acid/base characteristics, conductivity, and chemical catalysis. Here we have used a combined quantum mechanical and experimental approach to elucidate the precise proton topology of the Zr6-based framework NU-1000. Our data indicate that a mixed node topology, [Zr6(μ3-O)4(μ3-OH)4(OH)4 (OH2)4]8+, is preferred and simultaneously rule out five alternative node topologies. (Chemical Equation Presented).