Docking can only be performed at your home port.
The home port symbol is the "tilted anchor" All other ports with vertical anchors are refit locations for taking on fuel, minor repairs and torpedoes. Hull repairs can be made in Home port only.
When you are close enough to one of these ports a green anchor symbol will appear in the upper right hand corner. Do not over use the time clock while coming in. If you have set way-points and your last one is to close to land and your time compression is set to high you can accidentally drift your way right into the beach destroying your submarine.
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