Evolution of Spanish From Latin: Why We Say "el agua" and "las aguas"
"Water" is always "Feminine"!
OK, water is grammatically feminine... anyway, it's easy to see that agua is feminine, whether singular or plural in the two phrases: el agua fría and las aguas frías but they don't really satisfy student curiosity.
The explanation for nearly every question about Spanish etymology is found in Latin, and its evolution into Spanish over the past 1500 years or so (for some features, you can go back even farther in time). The Latin articles (really demonstrative adjectives) that became el, los, la and las were il, illa -- but they had many forms. The important form for understanding derivation of nouns in Spanish is the Latin accusative (direct object case), not the nominative (grammatical subject case). So in Latin, the water and the waters, in the accusative (singular and plural) were: illam aquam and illas aquas.
Over time, the final m of aquam and the final m of illam were weakly pronounced -- and since most people were illiterate, no one even knew that an m was supposed to be on the end of each of these words. Try pronouncing illa aqua and notice what happens to the second syllable of the article illa and its relationship to the first syllable of aqua. They blend into each other, or elide. What is left, in terms of what you hear? il aqua! It's easy to see -- even feel by pronouncing them one after another -- how il aqua became el agua.
Next, let's examine the accusative plural --the waters or illas aquas -- and see how it became las aguas. First, notice that the s at the end of illas prevents the final a of illas and the initial a of aquas from ever blending together? Also, the final s of aqua, is a strong marker of the plural. The initial i of illas was a briefly pronounced syllable (some people say it was a "short" i as in the English word is, but this is incorrect -- short and long in Latin have to do with length of pronunciation, not the quality of the sound). Anyway, it was weak and dropped out, leaving two L sounds, which in effect elided and left us with las aquas -- almost modern Spanish.
This phenomenon happens only with Spanish words that begin with a stressed a-, or ha-: águila (eagle) and hacha (axe) are two of the most common.