With river levels still very high across the region, more heavy rain is forecast, and communities are being urged to remain vigilant.
The amber warning for heavy rain is in place between noon tomorrow (Tuesday) and noon on Wednesday and covers western and central parts of the region including Hawick, Jedburgh, Peebles, Innerleithen, Selkirk and Galashiels.
Rain accumulations of 40-60mm are expected quite widely with some places possibly seeing 80-120 mm in a 24-36 hour period.
This could result in localised flooding, surface water on roads and has the potential to flood properties in at-risk areas.
Jim Fraser, emergency planning officer for Scottish Borders Council, said: “We have an amber weather warning in place over a 24-hour period and we are asking people in the western and central Borders in particular to be extra vigilant.
“Many of the areas affected by the bad weather on Friday and the weekend are expected to see even more heavy rain which will fall on already saturated ground.
"We also expect some of our rivers to rise quickly as the rain falls.
"Therefore, we could see flooding to roads and properties.
“Our emergency control centre is operational and we are working very closely with the Met Office, SEPA and a range of partners – including Police Scotland and Scottish Fire and Rescue Service – to monitor the situation and take action where needed.
"We will also engage with local Resilient Communities groups in areas that may need assistance.
“Please sign-up for free flood alerts from SEPA and be prepared to take action to protect yourself and your property if necessary.”
Yellow weather warnings for rain and wind are also in place from 2am on Tuesday through to 6pm on Wednesday for large parts of the Borders.
Check the SEPA website to sign up for free flood alerts relevant to your property.
You can also see details of the weather warnings on the Met Office website.