He said on the balance of probabilities, she had made an error of judgement in taking a sample when the swell was 3-4 metres.
"The weather conditions were such that it would have been very, very unsafe," he said.
Ms Gui had that morning logged into the laboratory and collected the bucket, thermometer and clipboard used for taking samples from a rock platform known as waterfall gutter.
The protocol required her to assess conditions before descending to the rock platform, and, if the water was breaking over the rocks, not to proceed.
Taking a sample involved lowering a bucket into the water from about 1m above water level, before taking the temperature and other readings.
Mr Guilford told the inquest it was unclear why Ms Gui continued to the rock platform, because in those conditions water would clearly be breaking over the platform.
"To us it's still somewhat inexplicable."
He said Ms Gui knew the protocol and was thought to be safety conscious by other students, who reported they were under no pressure to take readings in poor conditions.
Mr Guilford told the inquest the university had now stopped taking water samples from the waterfall gutter, and instead used electronic monitoring.
The decision was a difficult one, because the water temperature record had been taken the same way for the past 44 years, and was important to the discussion around global warning.
Mr Guilford said Ms Gui's death had been traumatic for staff and students at the laboratory.
Ministry of Business, Innovation and Employment inspector Chander Vasisht told the inquest the university had good protocols in place and had selected the sampling spot for its relative safety.
However they could also have put up further warning signs and identified the particular risks faced by those working alone.
Ms Gui was reported missing the day after taking the sample, but a search by police search and rescue and the police dive squad failed to find her.
Remains were found by divers the following month, and DNA testing was used to identify Ms Gui.
Coroner Shortland said he was satisfied with the safety protocols in place and the actions Auckland University had taken since the death, and made no recommendations.
He said Ms Gui's family had been involved in the early stages of the inquest, although were unable to attend today's hearing.