Zircons from three distinct granites within the Samphire Pluton, South Australia, are characterised at the micron- to nanoscale. Sensitive high-resolution ion microprobe (SHRIMP) U-Pb zircon dating generated 207Pb/206Pb weighted average ages of 1586 ± 9.3 Ma, 1583.2 ± 8.5 Ma and 1578 ± 9.5 Ma, respectively. Although zircons from all three granites display evidence of hydrothermal overprinting, this is most strongly expressed in a distinct, red-colored granite referred to here as Granite C. Alteration is expressed as variation in the concentrations of HREE + Y, Th and Pb, whereby grain margins are relatively enriched in these elements and both Zr and Si are depleted. Altered zircon cores have high U contents relative to grain margins, which are appreciably poorer in this element, whereas Th is strongly enriched within crosscutting microfractures. Coupled with the relative enrichment in non-formula elements and marked disturbance of U-Th-Pb isotope ratios, the nanoscale observations of Pb-bearing nanoparticles (galena?) implying mobility of Pb and other elements, nanofractures and structural defects demonstrate that zircon in Granite C has undergone multi-stage alteration impacting upon accurate dating. Importantly, and with implications for analogous systems elsewhere, our results confirm nanoscale open system U-Pb behaviour in Hiltaba Suite zircon. SHRIMP U-Pb zircon geochronology cannot confidently resolve any statistical differences in the age of the three granites, despite their distinct appearance suggesting they might represent temporally distinct phases of a larger magmatic system. Zircons within the most altered Granite (C), directly underlying the Blackbush uranium prospect contain convincing micron- to nanoscale evidence for an alteration event that triggered a remobilisation of uranium from granite into the cover sequence.