The Old Harbour was an old Time Lord city and starharbour just up to the dome of the Capitol.
A clock tower in the Old Harbour held the Oldharbour Clock, whose bells ran throughout the Gallifreyan day. The clockwork figures inside the clock tower developed sentience.
At the time of Omega's sacrifice, the room which would later become Archive Chamber 403 was a balcony overlooking the Old Harbour. (PROSE: The Infinity Doctors [+]Lance Parkin, BBC Books (1998).)