Why does "Akvo" not take the accusative?
Because of the preposition. After "en", nouns and adjectives only get the accusative marker if they show direction/motion towards ("into" instead of "in").
for example: la fisxo iras en la akvon
If "akvo" were to take any case, it would be the locative. The accusative is for the direct object of a transitive verb, the recipient of any action.
la fiŝo en la akvo estas
Is this ok or not ?
Yes, it's fine, though the order is peculiar. You might use it if people were confused about where the fish was.
La fiŝoj (plural) shouldn't have to be accepted here? The word "fish" (singular) can be used in English to describe a band of individuals of the same species, isn't it?
When do I have to use the accusative?
When I tried "la fiŝoj estas en la akvo", it didn't accept. Since the word "fish" in English is the same in plural, I think "fiŝoj" should be accepted there as well.
But the prompt in English is "The fish IS in the water", singular, not "The fish ARE in the water", plural.
Oh right! My bad