Because "agua" is feminine. In its singular state (agua), it uses "el" because "la" would be kind of awkward (it would get all mushed together). In the plural, though, it becomes "las aguas," and it's "agua fría," "agua profunda," "agua clara," etc.
Long story short: "agua" is a feminine noun with a masculine article in the singular form.
"The water is deep and clear" is "el agua profunda y clara". El can be a bit confusing sometimes because it also means "he". A way to remeber which one is which is if it is talking about something that would make more sense for a non human it will mean "it". If it is a person it means "he" Hope I helped with a bit of confusion!