Zircon has become an important archive of early Earth's history relating the surface water cycle and magmatism via its O isotope composition. However, metamictization of zircon presents a challenge when dealing with ancient detrital grains that are removed from their host rock. Here we use an extremely low-δ
18O zircon (−8 ‰) that is collected from an intact low-δ
18O host rock in order to refine our analytical approaches to O isotope and U
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Pb determinations. The δ
18O of the hosting quartz is −4.2 ± 0.4 ‰, attesting to the primary nature of low δ
18O values from an ancient water-rock interaction that originated in the Neoarchean. Highly variable
18O/
16O of the zircon correlate positively with
16O
1H/
16O measured by SIMS, representing secondary hydration accompanied by O isotope exchange, from the least altered δ
18O = −8.0 ± 0.1 ‰ to the highly hydrated domains with δ
18O around +2 ‰. Previously measured near-concordant in situ U
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Pb ages accompanied by high U (up to 0.5 wt%) present a puzzling observation of a preserved U
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Pb system and highly disturbed O isotope compositions. Here we test the accuracy of these interpretations by combining several “gold standard” techniques including elemental X-ray mapping, bulk laser fluorination (δ
18O), and chemical abrasion isotope dilution thermal ionization mass spectrometry (CA-ID-TIMS) for U
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Pb ages. The zircon bulk δ
18O values (−5.7 ‰ to −3.6 ‰) agree with the average values measured by SIMS, corroborating the effect of chemical removal of damaged domains by bulk that approach values in domains with low
16O
1H/
16O. Further, the triple O isotope compositions of zircon and quartz measured by laser fluorination have values similar to the isotope composition of the low-δ
18O protoliths found within the same area. The δD value of −175 ‰ measured in a bulk zircon with 2.4 wt% H
2O points to a near-surface source of hydrating waters. The CA-ID-TIMS U
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Pb dating of such highly metamict zircon is challenged by almost complete loss of the analyte during the chemical abrasion step and by U
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Pb discordant ages. Leaching at 130–210 °C for 3–12 h produces variably discordant ages, with one zircon grain yielding concordance and the
207Pb
206Pb age of 1773 ± 2 Ma after leaching at 170 °C for 12 h, whereas leaching at higher temperature for less time produced inferior concordance. Both normal and reverse discordance are observed, indicating high and near-contemporaneous mobility of U/Pb. Here we document both major and trace elemental mobility that are mechanistically difficult to explain, however both are related to a fluid-zircon interaction and are only observable by a combination of in situ and bulk methods.