Workers at Drumchapel Women's Aid had been part of the Scottish Government scheme for exemption from water charges in their former premises in Ledmore Street.
But after moving to a new site in Essenside Avenue in 2009, an admin error left them facing water charges of more than £16,500.
Refuge workers got in touch with the Scottish Water firm in charge of the billing, Business Stream, which resulted in £7483.14 being wiped.
However, that still left £9091.04 to pay, which the firm said represented the charges between the account being opened and the exemption being accepted on April 1 2012.
After a 17-month battle the bill has been scrapped.
Sandra Welch, who has worked with victims of domestic abuse for 21 years, said: "It's been horrendous having that hanging over us.
"We have spent a long time on the phone, and we have sent a lot of emails.
"We just kept saying we wouldn't pay it."
Ms Welch, who was a resident in the old refuge centre with her two children, said the drama had impacted on the service - but could have done far more damage if they had to pay it.
She said: "We have spent all this time trying to sort it out when we really need to focus on the people we help.
"We are a charity, every penny of funding we get goes to women and children.
"If we paid the bill it would have taken away funding from them.
"We are delighted. Now we can get on with our real jobs."
Another worker Louise McAleese said: "It would have impacted severely on women and kids suffering abuse.
"They were saying they would take it to the debt recovery.
"It was always at the back of or minds, it was hanging over us."
The refuge turned to Anniesland MSP Bill Kidd, who stepped in to support the charity.
He said: "I am delighted at the outcome, where a vital local service has been saved from having to pay these, for them, unscheduled payments."
A spokesman for Business Stream said: "We were happy to cancel Drumchapel Women's Aid's bill once it became clear that they were exempt from charges.
"Our advice to charities that are planning to move premises is to please get in touch early in the process."
Drumchapel Women's Aid offers 24/7 support. For information, call 0141 944 0201.