The Bebek Ferry
Bebek, a neighborhood beneath Boğaziçi University on the Bosporus is a 15-minute walk from the South Campus, has a ferry station. There are two kinds of ferries that use the dock, the city commuter ferry and a smaller ferry that makes a ring between villages on both shores of the Bosporus.
With the main city ferry line, you can go into the city in the morning and return in the evening.
On the schedule, orange is for week days, and blue for Saturdays, and red is for Sundays.
You can take the 8:00 in the morning boat and get to Eminönü by 9:00. This is a great way to avoid the traffic and get to the Tax Office when it opens.
There are boats in the afternoon coming back to Bebek, perfect for after a day after sightseeing. Times are underlined times for the return from Beşiktaş. Traffic can get crazy along the Bosporus in the evenings and especially on weekends as the summer approaches. You could take a minibus or bus from Taksim, get off in Beşiktaş, and come the rest of the way to Boğaziçi by ferry.