Sí Rhea, 

agua is a feminine noun but because two a’s in “la agua” come up against one another, they replace the la with el to make pronunciation easier i.e. el agua, which rolls off the tongue much better.  This particularly happens when the stress is on the first syllable of the feminine noun. 

Here is an excellent lesson which explains everything - there are a few tricky ones in there so be wary. Saludos. John

 Spanish feminine nouns starting with a stressed "a" sometimes use masculine articles and quantifiers