Dozens of homes were evacuated in Inverurie, Port Elphinstone and Ellon overnight as the swollen river sent flood waters racing down the streets.
Water also spilled from the River Ythan and teams from the Scottish Fire Service and the coastguard mounted an operation to rescue residents.
People were put up in rest centres while a number of local hotels also opened their doors to flooding victims free of charge.
Gauges in Haughton, just outside Inverurie, measured the Don at 5.6m (18.37ft) – the highest level for 45 years – while it measured 5.5m (18ft) at Parkhill in Aberdeen.
In Ellon, the Ythan stood at 4.4m (14.4ft) at its peak, 1.2m (3.93ft) above the previous record level in 1983, according to Scottish Environment Protection Agency (Sepa) figures.
Flooding in the north-east also brought major travel disruption, with busy roads closed and trains south from Aberdeen cancelled.
Part of the runway at Aberdeen Airport was damaged by the “unprecedented rainfall” and some passengers spent the night in the terminal as flights were cancelled.
The affected area has now been repaired and flights have resumed.
Police Scotland declared the flooding a “major incident”.
Chief Superintendent Campbell Thomson said: “Over the past 24 to 48 hours, and indeed the past week, we have responded to a number of flooding incidents and co-ordinated the multi-agency response to the adverse weather.
“A major incident was declared due to the severity of the warnings in place and the potential for serious impact on communities.
“Our focus over the past 36 hours has been the Donside area, Keith to Huntly, Turriff, Inverurie, Kintore, Ellon and into Aberdeen including Riverside Drive and the Grandholm area.
“Additionally, we continue to support the recovery effort in Deeside, specifically in the Ballater and Braemar area, following the impact of Storm Frank.”
There has been little respite for the north east since the New Year when Storm Frank brought flooding to villages around the River Dee, with Ballater particularly badly hit.
A Met Office amber warning for heavy rain has now expired but has been replaced with a yellow warning for snow and ice for much of Scotland, Northern Ireland, north west and north east England.
Richard Brown, head of hydrology at Sepa, said water levels around the River Don were “pretty exceptional”.
He added: “We have had a gauging station up at Alford for the last 42 years and it has exceeded anything we have ever recorded.”
NHS Grampian have raised concerns over private water supplies in Aberdeenshire and urged residents to drink bottled water.
A spokesman said: “If a private well or spring has been covered by floodwater, proceed with caution and contact Aberdeenshire Council for advice.
“While waiting for an answer or if you are in doubt, assume the water is unsafe to drink and source bottled water.”
There was some relief during the flooding as missing camper Terence Kilbride, believed to have been swept away by flood waters from the Dee, was found by police safe and well.
Scotland’s Deputy First Minister John Swinney said: “The impact of this latest round of flooding is causing transport difficulties and putting properties at risk of flooding.
“The Scottish Government’s resilience committee is monitoring the situation very closely and we have discussed the unfolding events and work to mitigate the impacts and ensure the safety of people in local communities.”