Robert Leeming, 34, was first arrested days after Jasmine Lovett, 25, and her daughter Aliyah Sanderson were reported missing.
He was released by police but was later rearrested after their bodies were discovered in woodland near Calgary on Monday.
Mr Leeming, who has lived in Canada for six years, denied any involvement.
Following his initial arrest, he told local media that he was “traumatised” by events.
He claimed to have been romantically involved with Ms Lovett, who was living with her daughter as a tenant at his home, in the Cranston district of Calgary.
Ms Lovett’s family said their lives had been “devastated and our hearts are heavy” following the discovery of their bodies.
The mother and daughter were last seen alive in Cranston on the evening of Tuesday 16 April.
Activity on Ms Lovett’s bank accounts stopped on 18 April.
Mr Leeming, who is believed to be from Stoke-on-Trent, was arrested a week later, but was released by police after being questioned.
A Calgary Police spokesman said on Monday: “At approximately 4am today we located the bodies of a woman and child, believed to be that of Jasmine Lovett and Aliyah Sanderson, in Kananaskis.
“A suspect has been taken into custody and charges are pending.
“The suspect cannot be named by police until charges are officially laid by the Justice of the Peace.
“However, police can confirm the suspect is the same man who was taken into custody two weeks ago.”
Post-mortem examinations are due to take place, although the cause of death is not expected to be released.
Ms Lovett’s family said in a statement: “Our lives have been devastated and our hearts are heavy.
“We are trying to understand how this tragedy could have happened to our loved ones.”