In the sentence:
They also live in Argentina, Bolivia and Ecuador where they reside mainly on estuaries, lagoons, mud flats and salt lakes.
we can distinguish two clauses. The main clause:
They also live in Argentina, Bolivia and Ecuador.
and a subordinate clause:
where they reside mainly on estuaries, lagoons, mud flats and salt lakes.
Note that the meaning of the main clause doesn't change if the subordinate clause is removed.
The following is my understanding of the usage of comma and "where" that I have come across:
A comma is advised if the where-clause can be removed without altering the meaning of the main clause. For example:
I first saw him in Paris, where I lived in the early sixties
A comma is not advised if the where-clause cannot be removed. For example:
This is where I live
Hence, in the OP's quote I would use a comma:
They also live in Argentina, Bolivia and Ecuador, where they reside mainly on estuaries, lagoons, mud flats and salt lakes.