Sounds like it could be James White's The Watch Below. One reviewer's summary says,
A cargo ship is torpedoed in World War II, and goes down to the bottom with a small nucleus of survivors, male and female. They are not killed; instead they survive, and manage to live the rest of their lives out on the bottom of the sea floor, existing on the food supplies stored in the hold and water reclaimed from condensation. They even have children and grandchildren. This story is superimposed over the tale of the migration of a species of aquatic aliens who have created an armada to escape the destruction of their home planet.
You might recognize other plot elements from a more-detailed review.
It was first published in 1966 and has been in and out of print since then, in several editions.