Her husband is British real estate heir, Justin Portman, a half-brother of the 10th Viscount Portman, son of a Viscount and Scion of one of Britain's wealthiest real estate families, owning swatches in London. The couple had their first son, Lucas Alexander, on December 22, 2001. On September 1, 2002, Vodianova and Portman married in a lavish ceremony in Saint Petersburg. Their second child, daughter Neva (named after the Russian river Neva) was born on March 24, 2006, weighing 7 pounds. She posed with her baby in Vogue. Her third child, a boy named Viktor, was born on September 13, 2007; Viktor is named after Natalia's grandfather. Vodianova's husband and children often travel with her.

Vodianova is also a dedicated philanthropist, an achievement that was honored in the March 2007 issue of US Vogue.