This is a really interesting concept and I love the theme. As a fellow latino (Argentina) I really love to see the call to action regarding this problem. Thinking about our cities and the potential green spaces we can restore to help alleviate problems like flooding is great and I love the phrase "What lives beneath the city, unseen, shapes its surface". The mechanics are clear and straightforward. I would love to have more reference images of the trees and seeds, while also adding some of the art that inspired you. I don't know if the music, sound effects are a big concern as you can use free assets for this matter, but I get that you have a very clear vibe (Brazilian music) going on.

I'm worried, however, that the amount of content you have in mind is too much for the Scope of the jam. Personally, I would scrap the idea of having the daytime as different levels and focus on one thing there. Like a damaged city landscape, flooded with both water and grey buildings (although I know Brasil is really colorful). As you explore the underground and plant seeds there, the daylight scene changes to match the actions the player does.

An idea regarding the loss condition, you can check a game called The Swindle. There you have a set amount of time (in days) until a thing that prevents burglars becomes operative. Each completed level is a day, if you lose (you are killed) it also takes a day. You can exit the level early if it proves too difficult. Maybe the daylight scene is about too flood unless you get the Mata Atlântica trees planted. If you fail at the night part of the game, the days go by.