His body was so deep that it couldn't be retrieved for either of the three reasons:
A. The water pressure would probably crush anyone who tried to retrieve his corpse.
or
B. His body was too deep down for it to even be seen, as there is no light at the bottom of the ocean. With no way to track him (because he is dead, and his chakra is gone) it would be impossible to find his body in such darkness.
or
C. Submarines weren't even invented yet, so no one would have the lung capacity to get far enough to retrieve the dead body. Of course, he could have sent an Edo Tensei but then there's still A and B to take into consideration. Besides, who would go through all of that trouble to retrieve a corpse when they already have Madara Uchiha. Having Madara Uchiha in his clutches made getting Jiraiya irrelevant.
