Manokwari is small enough to walk around the city centre, but ojeks (motorcycle taxis) are the quickest way to reach beaches, the university area, and the foot of Gunung Meja. Agree on the price before you get on — short trips around town cost a few thousand rupiah. Minibuses (angkot) run fixed routes along the main roads and are very cheap. For the Arfak Mountains or Anggi Lakes, you'll need to hire a vehicle with driver; ask at your accommodation or around the port area.
Speedboats to Mansinam Island and other bay islands depart from the main harbour. Negotiate prices with the boatmen directly and agree on a return time.