Just because you set the sub to a set knot speed, doesn't mean it'll actually cover that distance in that time. There are ton of currents going in all different directions.

Dead reckoning which is usually hit or miss on the surface but better than nothing. Probably worse under the water. It's why all these subs that dive to Titanic have to drop down until they hit the floor and then swim around until they find a landmark that points to the ship. They only have a rough idea of where they are when they get to the bottom.