It flows generally southwest from its origins near Glen Afton and Glen Massey, west of Ngāruawāhia, to reach a northern arm of Raglan Harbour (see 1:50,000 map).

Its main tributary is Kahuhuru Stream, which Highway 22 follows for several kilometres.

The lower river flows over Puaroan age (about 150 million years ago), blue-grey Puti siltstone.

[2] The Waingaro River is one of the largest sources of sediment in Whaingaroa Harbour, partly because it is 99 percent unfenced.

[3] Pollution has been worsening for phosphorus, though nitrogen has improved, as shown in this table of important (i.e. slope direction probability over 95% and RSKSE over ±1% pa) improvements, or deteriorations (-) in relative seasonal Kendall slope estimator (RSKSE) trends (monthly records are flow-adjusted using a Lowess curve fit with 30% span.)