About half the river's course from its sources on the edge of the Rangitoto Range is through deep valleys and gorges formed of Late Jurassic to Early Cretaceous Manaia Hill Group greywacke (a form of sandstone, with little or no bedding, fine to medium grained, interbedded with siltstone and conglomerate, and with many quartz veins), which is buried in many places by Quaternary ignimbrites.

The main ignimbrite is the Ongatiti Formation, up to 150 m thick of compound, weakly to strongly welded, vitrophyric, including pumice-, andesite and rhyolite lavas.

Initially these are mainly the Late Quaternary Piako Subgroup, which includes Late Pleistocene alluvium, and minor fan deposits of unconsolidated to very soft, thinly to thickly bedded, yellow-grey to orange-brown, pumiceous mud, silt, sandy mud and gravel, with local muddy peat.

Finally, the river flows mostly over the Holocene floodplain, where the alluvium and colluvium consist of variously coloured, unconsolidated sand, silt, mud, clay, local gravel and thin intercalated (a form of interbedding, where distinct deposits in close proximity migrate back and forth) peat beds.

[5] The Puniu is 6th dirtiest out of 13 sampling points in the Waipa catchment, with unsatisfactory nitrogen, phosphorus and turbidity levels.