Hello, and welcome to the forum. Agua is always feminine, but it takes the masculine definite article ( el) when in the singular because the word agua begins with a stressed A. All words that have the emphasis on the first syllable and begin with an A follow this patter. If they didn't the end of la would run together with the first syllable and sound like lagua. Despite using the masculine definite article in the singular, it is never actually masculine. You still say el agua clara, with a feminine adjective. It revers to the feminine article in the plural, las aguas claras, because the S separates the two A sounds.
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Slightly off topic, but think of English. We use 'an' in front of vowels. So we (usually) speak of a hospital or a hotel, but an heir or an heirloom. The h in 'hospital' is stressed, so we stick an 'a' in front of it.
The h in 'heir' is not pronounced/stressed, so we add the n to form 'an heir'. I.e., we change the rule ('an' only goes in front of vowels) so that things sound better. That's the same reason for having el agua, as Mariana and Macfadden explain.Sometimes it's easy to think of Spanish as complicated and weird, without realizing that we do similar complicated or weird things in English - it's just that, as it's our language, we're simply not aware of it.