Born in Dunedin, Cotton was educated at Christchurch Boys' High School, where he lost the sight in his left eye because of a schoolmate's prank.

In 1908 Cotton graduated from the University of Otago with an MSc, with first-class honours in geology.

[1] In the 1959 Queen's Birthday Honours, Cotton was appointed a Knight Commander of the Order of the British Empire.

[2] According to Cotton himself an important development to his scientific career was the introduction of air mail to New Zealand allowing letters to arrive or be received from Europe within two weeks.

The building on the Kelburn campus contains a low-rise block with science departments, a group of lecture theatres and laboratories and "Cotton Street", an enclosed concourse with shops and displays.