I always figured Mary Jo was pregnant or going public. That would explain the convenient shallow water that Ted escaped from and Mary Jo drowned in.
Mary Joe Kopechne’s body was found in a position that implied that she was struggling to keep her head out of the water. Once Teddy’s car turned upside down, she did not immediately die; she was alive and then suffocated rather than drowned, slowly, as the water seeped in, for 11 hours.