Rambam gives his explaination in the Guide of the Perplexed, Book 2, Chapter XXX:
It is also important to notice that the words," And God called a
certain thing a certain name," are invariably intended to
distinguish one thing from others which are called by the same
The first Choshech, in verse 2 (וְחֹשֶׁךְ עַל פְּנֵי תְהוֹם), denotes the element fire, where as in verse 5 (וְלַחֹשֶׁךְ קָרָא לָיְלָה) Hashem uses Choshech the way we typically use it, the sense of "darkness".
The element fire is called Choshech because it is not luminous, it is
only transparent; for if it were luminous we should see at night the
whole atmosphere in flames.
Eretz, in the first verse (אֵת הַשָּׁמַיִם וְאֵת הָאָרֶץ) means general matter, and in verse 10 (וַיִּקְרָא אֱ־לֹהִים לַיַּבָּשָׁה אֶרֶץ) it is distinguishing as the word used to refer to the specific matter our planet is made of.
We must further consider that the term erez is a homonym, and is
used in a general and a particular sense.
In verse 8, Hashem makes a distinction between the form of Rakea (וַיִּקְרָא אֱלֹהִים לָרָקִיעַ שָׁמָיִם), and the form of Shamayim from verse 1 (אֵת הַשָּׁמַיִם וְאֵת הָאָרֶץ), which are commonly used interchangeably.
There is one common element of "water" which is distinguished into three forms: seas, firmament and 'over the firmament' (water by name, but not form). "Water" in the first verse (אֵת הַשָּׁמַיִם וְאֵת הָאָרֶץ), does not refer to the water which forms the seas, I think "fluid" would be a better translation for the first "water", while "water" in verse 10 (וּלְמִקְוֵה הַמַּיִם קָרָא יַמִּים), the water in the seas, is ordinary water.
The phrase," And he divided between the waters," etc., does not
describe a division in space, as if the one part were merely above the
other, whilst the nature of both remained the same, but a distinction
as regards their nature or form.