Maybe some geology buffs can correct me, but as I understand it there has been three periods with ocean on top of the crust we call Pakistan today. The Proto-Tethys, Paleo-Tethys, and Tethys Ocean. Many hundreds of millions of years of being ocean.

Because of the Indian subcontinent colliding with the Eurasian plate there's a wide variety of origins for the surface geology in that region.

An incredibly detailed and descriptive map:

https://upload.wikimedia.org/wikipedia/commons/5/52/1964_Pak...