It seems like Bruges was built more inland for the same reason that [Amsterdam] (http://en.wikipedia.org/wiki/Amsterdam) was built inland with an impressive canal system. The land there is low lying, and thus more susceptible to flooding. The canals are probably easier to control the water levels further inland.

Hey, I asked a question about the siting of Rome a while back. The short answer, there was a ford across the Tiber there, making it a place people had to go if they were traveling north-south.