Preferential removal of W relative to other trace elements from zoned, W–Sn–U–Pb-bearing hematite coupled with disturbance of U–Pb isotope systematics is attributed to pseudomorphic replacement via coupled dissolution reprecipitation reaction (CDRR). This hematite has been studied down to the nanoscale to understand the mechanisms leading to compositional and U/Pb isotope heterogeneity at the grain scale. High-Angle Annular Dark Field Scanning Transmission Electron Microscopy (HAADF STEM) imaging of foils extracted in situ from three locations across the W-rich to W-depleted domains show lattice-scale defects and crystal structure modifications adjacent to twin planes. Secondary sets of twins and associated splays are common, but wider (up to ~100 nm) inclusion trails occur only at the boundary between the W-rich and W-depleted domains. STEM energy-dispersive X-ray mapping reveals W- and Pb-enrichment along 2–3 nm-wide features defining the twin planes; W-bearing nanoparticles occur along the splays. Tungsten and Pb are both present, albeit at low concentrations, within Na–K–Cl-bearing inclusions along the trails. HAADF STEM imaging of hematite reveals modifications relative to ideal crystal structure. A two-fold hematite superstructure (a = b = c = 10.85 Å; α = β = γ = 55.28°) involving oxygen vacancies was constructed and assessed by STEM simulations with a good match to data. This model can account for significant W release during interaction with fluids percolating through twin planes and secondary structures as CDRR progresses from the zoned domain, otherwise apparently undisturbed at the micrometre scale. Lead remobilisation is confirmed here at the nanoscale and is responsible for a disturbance of U/Pb ratios in hematite affected by CDRR. Twin planes can provide pathways for fluid percolation and metal entrapment during post-crystallisation overprinting. The presence of complex twinning can therefore predict potential disturbances of isotope systems in hematite that will affect its performance as a robust geochronometer.