The actor said the couple's main concern is their 11-month-old daughter, Aven.
"Things happen in life and you just have to roll with it," he continued. "I wish things could have been better but our focus is on our daughter."
"They have been separated for a while now," a source told the mag, adding that legal proceedings have begun, but divorce papers have not been filed.
Despite the couple's relationships woes, the source said, "the baby is doing great… both parents are devoted to their child, Aven is still a part of Matthew's everyday life."
In addition to his role as Rufus on "Gossip Girl," Settle is also set to make his Broadway debut as fast-talking lawyer Billy Flynn in "Chicago." He will star in the role from March 29 - June 6 in NYC.
Settle, 40, and Nativ, 26, married in July 2006.
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