Detrital zircon in six surface samples of sandstone and contact metamorphic quartzite of the Magaliesberg and Rayton formations of the Pretoria Group (depositional age c. 2.20–2.06 Ga) show a major age fraction at 2.35–2.20 Ga, and minor early Palaeoproterozoic – Neoarchaean fractions. Trace-element concentrations vary widely, with Ti, Y and light rare earth elements (LREEs) spanning over three orders of magnitude. REE distribution patterns range from typical zircon patterns (LREE depletion, heavy REE enrichment, well-developed positive Ce and negative Eu anomalies) to patterns that are flat to concave downwards, with indistinct Ce and Eu anomalies. The change in REE pattern correlates with increases in alteration-sensitive parameters such as Ti concentration and (Dy/Sm) + (Dy/Nd), U–Pb discordance and content of common lead, and with a gradual washing-out of oscillatory zoning in cathodoluminescence images. U and Th concentrations also increase, but Th/U behaves erratically. Discordant zircon scatters along lead-loss lines to zero-age lower intercepts, suggesting that the isotopic and chemical variations are the results of disturbance long after deposition. The rocks sampled have been in a surface-near position (at least) since Late Cretaceous time, and exposed to deep weathering under intermittently hot and humid conditions. In this environment, even elements commonly considered as relatively insoluble could be mobilized locally, and taken up by radiation-damaged zircon. Such secondary alteration effects on U–Pb and trace elements can be expected in zircon in any ancient sedimentary rock that has been exposed to tropical–subtropical weathering, which needs to be considered when interpreting detrital zircon data.