There are a few ways to track a sub. There are of course communication frequencies that can be identified. There are transponder codes that identify each sub; however, going deep may affect both of these. However, each sub has it's own plant signature, that is to say, it has unique sounds that can be identified by the ships computer and even the operating crewman. If you're familiar with automobiles a little, you know Ford's, GM's and Dodge's all have uniquely different sounds. Drilling down further, a sophisticated computer and a highly trained professional can tell you among numerous Camaro's, which sound is Camaro 1, Camaro 2, etc.