This is mere speculation but I will put it in spoiler tag in case you don't want to be spoiled
Harry may have had an affair with Dexter's mother, but we never know for sure. What we do know for sure is that Harry is not Dexter's biological father. That was established in Season 1, episode 9, "Father Knows Best." It was revealed in that episode that Dexter's biological father had just died. Dexter goes to his house to get his belongings and discovers an old thank-you note he had sent his blood donor years ago. Dexter has a rare blood type AB- and Harry got Dexter's father to donate blood when Dexter was young and needed a blood transfusion. He never told Dexter that his biological father donated the blood. Dexter always thought his biological father had died when he was a kid.