Modern submarine use several methods of navigation; a common misconception is that they use Sonar to navigate, but that's limited and not practical, except in a very few circumstances.
All submarines use charts (corroborated with dead reckoning plotter and fathometer soundings), satellite (GPS), electronic gyro, visual references, radar (close to shore), for primary navigation in most oceans. On rare occasions, uncharted mountains or navigational screwups have led to submarine accidents. My own boat hit an underwater mountain in the Mediterranean in 1977; the USS San Francisco hit an uncharted mountain a few years ago.
The main periscope can also be fixed with a sextant if necessary to get a star fix or to take a sun line. Of course the Navigator can also do it the old fashioned way and take a sextant to the bridge while on the surface as well. There are always multiple backups for all submarine systems.
GPS is the primary method of navigation; sensors are located within the main periscope, (along with lots of other cool stuff). Navigational fixes are taken at periscope depth when a boat is doing routine housekeeping operations (e.g., trash disposal, receiving radio traffic, blowing sanitary tanks, etc.). However, no one fix, even GPS, is taken at face-value; fixes are taken from each navigational system, and then checked against each other for accuracy by the Quartermasters. The results are then reported to the Navigator.
The reason for cross-checking is because electronic systems are not infallible. It was this error that led to my boat's accident in '77.
At that time, there were several systems in place as there are today; the boat was in the Mediterranean Sea, and was carrying a replacement Quartermaster. Rather than follow proper procedure (as it turned out during the post-accident investigations and courts-martial) he trusted only one system for a fix, which was hyper accurate on his own boat. However, at the time, that system on my boat was malfunctioning. He also failed to report his findings to the Navigator. When the analysis was done later, it showed that the boat was almost 2 miles off course. The QM's dereliction was the only reason that the CO, XO, and the Navigator weren't relieved of their positions, as is customary in such cases, particularly with nuclear vessels. Typically it is a career-ender for all officers involved.
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