Grammatical genders are just that. Grammatical. It's a classification scheme. Latin had neutral nouns and plenty of languages make grammatical differences between animate and inanimate nouns. That current romance languages make a deliberate division between "male" and "female" nouns does not mean they have to correspond to actual features of human beings.
That being said. It's ridiculous that agua is femenine but with the definite article it has to be el agua in singular but las aguas in plural. All the explanations by RAE simply amounts to "we like it this way, lolol".
Why. Just why? It's just you French and your obsession for...
la silla vs el asiento (Spanish)
Fuck.