Bismihi ta'ala

Prior to anything, we must first establish whether the narration is authentic, as far as the text and the chain as well. 

If we were to assume it's all good as far as its issuance from a Ma'sum (a.s.), then we most certainly cannot take it in its literal meaning, and it must be interpreted in such a way that would make sense. Whale could refer to the orbit, maybe because the whale's back is not flat, and for the earth, it has "the equatorial bulge", the water could refer o space, rock could refer to planets, and so on.

Some of these explanations have been given in commentaries on al-Kafi. 

The Imam (a.s.) is duty-bound to say things that are not above or beyond people's comprehension at that time. There could be words omitted for brevity, like how the Quran addresses people and certain things. 

The following is a good detailed answer (in Arabic) from the holy Shrine of Imam Husain (a.s.):

https://alrasd.net/arabic/islamicheritagee/3590

And Allah ta'ala knows best