Why is 'agua' feminine if you say 'el agua'?

The word 'agua' is indeed feminine, although we use the masculine article 'el' with it to avoid something called cacophony, which basically means it sounds bad or uncomfortable if we use 'la'. This applies to feminine words that begin with a stressed /a/, so if you look at agua, you'll notice it begins with an /a/ sound and the emphasis falls on that syllable. Thus, instead of 'la agua', which can sound a bit of a mouthful, we say 'el agua' instead.
Similar words like this are el hada, the fairy, or el aula, the classroom.