Meg and Will were in a committed relationship for several years, even living together. However, they broke up shortly before Will was recruited into the Sanctuary Network, and Meg moved out of their apartment.
Will later called her from the Sanctuary to hear if she was well. Meg was concerned because he seemed to have disappeared completely, but was happy to hear that he enjoyed his new job and could finally sleep well. Based on how "good" he sounded, she suspected Will to have a new girlfriend, and hung up on him.
When Abby asked him about his past relationships, Will told her about Meg, as well as about Clara Griffin.