Homes in Inverurie and Ellon had to be evacuated as the non-stop downpour caused the Rivers Don and Ythan to burst their banks.
Around 38 properties in Port Elphinstone - also affected earlier in the week - had to be evacuated and people were moved from 18 homes in Ellon.
Homes in the Meadows area of Ellon had to be evacuated as the Ythan finally broke its banks after running at a high level all week.
In Inverurie the scenes in the town were described as the worst in living memory.
Local photographer Paul Douglas said: “I was taking to one man who’s lived here all his life and he said he’d never seen anything like it.
“The town had been bracing itself for the Don to burst its banks but when it did the torrent was unbelievable.
“Port Elphinstone has been particularly badly affected. I was here earlier in the week and the water levels on the properties are even higher.”
One local resident, who declined to be named, said: “It’s heartbreaking to see what’s happened.
“The water just cascaded into the Port. I’ve never seen anything like it.
“We were bracing ourselves for the worst but when the river burst it was a complete nightmare.”
The situation on the roads in the North-east is also chaotic with many routes closed, particularly parts of the A90 between Peterhead and Aberdeen, due to flooding.
More than 30 schools in Aberdeenshire have been closed or partially shut.
Transport has also been disrupted with trains to and from the central belt starting and terminating at Dundee.
The runway at Aberdeen International Airport has reopened following repairs during the night.
NHS Grampian released the following advice for those with private water supplies across Aberdeenshire: “If your water is a private supply such as a well or spring, then check that it has not been affected by floodwater. 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.
“Boiling water kills pathogenic bacteria, viruses and parasites but does not remove harmful chemicals, which is why using bottled water is recommended.”