Severe flood warnings covering the River Mersey in Didsbury and Northenden have now been lifted, the Environment Agency has said.
Warnings covering the upper River Irwell area - for Oldham, Bolton, Rochdale, Haslingden, Ramsbottom and Rawtenstall - and for the lower Irwell have also been taken off the official list.
The news came at around 9.30am after a night of fear for many.
READ MORE: Dozens of trees fall and block roads as region battered by Storm Franklin
Council bosses, however, said emergency evacuation operations have now been stood down.
A flood 'alert' remains in force for the areas, and the council said it would likely continue through the week until the Didsbury flood basin empties.
Severe flood warnings were in place for the River Mersey in East Didsbury, and at West Didsbury and Northenden, after Storm Franklin brought heavy and persistent rain.
In a morning update for both areas, the Environment Agency said: "This severe flood warning has been removed.
"However, a flood alert for the area remains in place, meaning that there is a possibility of flooding to properties.
"The Environment Agency will continue to monitor the situation and will inspect the area for any other impacts.
"Please be aware that there may still be risks around the River Mersey due to high river levels.
"Please do not attempt to drive through flood water and avoid using low lying footpaths."
Properties in West Didsbury and Barlow Moor, around Princess Road, Riverside Avenue and Mersey Crescent, were said to be at risk.
The warning covered homes on Stanton Avenue to Palatine Road, and around Kenworthy Lane and Ford Lane in Northenden.
Around the Mersey in East Didsbury, the warning covered Millgate Lane and Parrs Wood Road, including Tuscan Road to Broad Oak Lane, as well as properties around Kingsway, Wilmslow Road, Merston Drive, Millgate Farm and the Old Bedians sports centre.
Councillors said 430 homes were at risk of flooding and a rest centre was set up at Didsbury Mosque.
But Manchester City Council leader Bev Craig confirmed emergency evacuation operations have been stood down in Didsbury.
She wrote on Twitter: "Thankfully after the peak at 4am, emergency evacuation operations on the ground were stood down and we got through the night without any flooding or damage to properties.
"Thanks again to everyone involved and to the hundreds of residents who were impacted."
In a statement, coun Craig added: "It is welcome relief that the severe flood warning has now been removed for the River Mersey around West Didsbury and Northenden. However, a flood alert remains in place and will do most likely through the week until the flood basin in Didsbury empties.
"We're also expecting continued wet weather in the coming days and a Met Office weather warning is still in place. So please be careful if you need to travel today and through the week.
"Thankfully, because of the skilled management of the flood defences on the River Mersey, major flooding and formal evacuations have been avoided, but as the weather remains unsettled there will likely be disruption on our roads and transport routes, so make sure you check the relevant websites before you travel, take care and give yourself extra time.
"We owe a huge debt of thanks to staff at the Environment Agency, emergency services and volunteers who have worked with council staff overnight to monitor the risk of flooding and keep us safe. Water levels look to be falling but this will remain under review for the next few days, so keep an eye on information from the council and emergency services."
Flood warnings remain in force covering the River Mersey at Chorlton and Sale golf clubs, Chorlton Water Park and Stretford, Fletcher Moss and Withington golf course, as well as for the River Roch at Littleborough, Rochdale.
