[sc_rufctr]

One word - Sound - They go to extraordinary lengths to mitigate sound in a submarine.

They're always working on something new but as far as I know that's the only reliable way they can track a submarine. (I'm sure Mr SeaHawk will chime in shortly.) There are "new fangled micro torpedoes" (less than 10 foot long) that pose a real threat but a submarine at depth is very hard to detect and deal with.

Your nuclear powered submarines can stay submerged for a very long time. They make their own air and water. Their only real limitation is the amount of food they can store onboard for the crew.