The first European exploration of the Waitangiroto was on 30 December 1865, when surveyor Gerhard Mueller took a waka and paddled up what he called the "Waitangi-Roto", in search of a lake he had been told by local Māori was fifteen or twenty miles inland.

[2] Mueller navigated six miles up the river before it branched into many small arms and his route was blocked by fallen trees.

He noted there was dense bush on both sides, "beautiful Kowhai trees abounding and almost all shrubs in flower…"[2] He also came across a "cranery": a nesting colony of the kōtuku (Ardea alba modesta):"Of these birds (near 4 ft. high) imagine seeing around you from 50 to 60, sitting on high pines and lower trees, in a circle of about 150 yards, their pure white feathers shining in the sun.

"[2]The Waitangiroto Nature Reserve, located on the river, is the only nesting area for kōtuku in New Zealand.

[3] In 1967, a major flood caused the Waitangitāhuna River to breach its banks and establish a branch with a new course to Lake Wahapo.