This caution comes from Stuart Khan, associate professor at the school of civil and environmental engineering at the University of NSW, who has been telling the state government for three years that it should never let Warragamba rise to full – because ample space is needed for flood mitigation.

"I do get worried because I always look back at what happened in July 1998 … [when] about a thousand gigalitres flowed into that reservoir over about a couple of weeks," Associate Professor Khan said.

"It was just pure lucky that … Warragamba was half empty. There was a thousand gigalitres of space to hold that water.

"If the same inflow of water happened now … with the dams already full, western Sydney would be devastated. Penrith would be flooded, right down the Hawkesbury River … Essentially from Penrith all the way down to Richmond you would have major flooding going on."

A 2011 report commissioned by the then planning department found that as many as 22,000 people would not have time to evacuate in some flood scenarios because of inadequate exit roads.

The government initiated the Hawkesbury-Nepean Valley Flood Management Review in early 2013 in response to extensive flooding across south-eastern NSW the previous year, when Warragamba Dam spilt for the first time in 14 years.

After heavy rains this week, water started spilling once again over the Warragamba Dam wall about 7.30am on Thursday.

The government's review is still running but its first stage concluded there was no "simple solution or single infrastructure option that can address all of the flood risk in the Hawkesbury-Nepean Valley floodplain".

However, Associate Professor Khan says there is a solution: controlled releases of water from the dam, so it never approaches full. Sydney needed to make decisions that served both its water supply security and its flood risk.

Associate Professor Khan had opposed the building of the desalination plant, but now that it is there – and costing about $500,000 a day to keep on standby – he says authorities should factor in its potential to supply at least 15 per cent of the city's water needs.

That would already be enough to ensure Warragamba Dam never needed to be above 85 per cent full – "and that is still a huge volume of water".

More than half of the capacity of Brisbane's Wivenhoe dam is reserved for flood mitigation, 1450 gigalitres to 1165 gigalitres for water supply. That is explained by the historical purpose of both dams, Associate Professor Khan said.

"Wivenhoe was constructed after the 1974 flood and because of that flood, largely, as a flood-mitigation reservoir, whereas Warragamba was built [in the 1960s] because Sydney was running out of drinking water."

It is time that Warragamba served both needs, he argues.

The state government's emergency planning for the basin is based on a repeat of a flood in 1867 that inundated 200 square kilometres of north-western Sydney including Windsor, Richmond, Pitt Town and Riverstone and covering the present-day suburbs of Bligh Park and McGraths Hill.

"At some time in the future, a flood of this magnitude will occur," SES flood risk expert Steve Opper told Fairfax Media in 2013. "It is not a question of if; it is a question of when."

The water level at the Windsor Bridge, usually about 1.5 metres, reached about 19.2 metres in 1867 and 13.4 metres in a 1990 flood. Warragamba Dam, if it failed, would only add to the natural disaster threat.

After the devastating April floods in NSW, State Emergency Services deputy commissioner Steven Pearce told Fairfax Media: "Looking at the evacuation modelling, we would have to start evacuating the population at least 12 hours before the weather event even arrived.

"But as the population has grown, the infrastructure to evacuate – specifically roadway routes – just haven't kept up."

Emergency Services Minister David Elliott then acknowledged that disaster would inform thinking on the Hawkesbury-Nepean plan.

The priority of stage two of the planning has been preparing communities and businesses in the Hawkesbury-Nepean Valley for future flood and involved cost-benefit assessment of flood mitigation options.

However, Associate Professor Khan said: "Couldn't we just manage this reservoir [Warragamba] slightly differently, given the huge imbalance between supply security and flood risk; that we try to prevent that flood from happening, rather than work on a solution of how we get people out of there when it does."