Rutherford married Carlos Tarajano, a Venezuelan banker, in June 2001. Tarajano was diagnosed with a heart condition soon afterwards. Rutherford filed for divorce in January 2002, after six months of marriage. The wedding was featured shortly thereafter in the February 2002 issue of InStyle magazine. Tarajano died in 2004.
Rutherford married her second husband, German businessman Daniel Giersch, in August 2006. She gave birth to their first child, son Hermés Gustaf Daniel Giersch, in October 2006. While pregnant with their second child, Rutherford filed for divorce from Giersch on December 30, 2008. Rutherford and Giersch subsequently became involved in a child custody dispute over their son and unborn child. Rutherford gave birth to their second child, daughter Helena, in June 2009. Giersch claimed he was not informed of the birth by Rutherford, and became aware of it only through media reports. In August 2009, Rutherford and Giersch reached a temporary settlement of joint legal and physical custody, in effect until April 2010. Rutherford also obtained a temporary restraining order against him the following month. Giersch's American visa was revoked in April 2012, after Rutherford's lawyer informed the State Department about issues pertaining to Giersch's businesses, which led the Department to conclude that they had sufficient evidence to deport him. It has been reported that the allegations involved fraud or an involvement in drugs and weapons dealing in South America, considered terrorism under the Victory Act. Giersch consequently became unable to enter the United States, and took up residence in France and Monaco. In May 2012, Rutherford and Giersch's children went to France to spend the summer with their father. Rutherford asked the court to grant her sole custody so that she could keep the children primarily in the United States following their visit to France, as the existing joint custody agreement required her to travel frequently to enable Giersch to spend time with the children. In August 2012, in a widely reported decision, a California Superior Court judge ruled that the 50/50 custody arrangement should remain, and that because Giersch is unable to travel to the United States, the children should live in France with him and attend school there, with Rutherford travelling there to visit them. Though Rutherford opposed the decision and requested a stay of proceedings while she appealed, her request was denied and it was ruled that in two years, Giersch's eligibility to enter the United States and the consequent well-being of the children will be reassessed.
In June 2013, Rutherford filed for bankruptcy, claiming debts of approximately $2 million, primarily due to the $1.5 million she spent on legal fees relating to the divorce and custody dispute with Giersch.