I can't remember the name of the manga, I know it went something like "High School Past time" or something. The cover I mostly saw used for it was of the three girls, the one with the glasses in the foreground, in swimsuits, holding a water pistol, the background an urban environment flooded with water.

Basically, some alien monsters came and made everyone vanish but the protagonist and three girls, one of whom wears glasses, the second has a ponytail and the third is small child. The MC is a genius and grows plants and builds stuff for them to live comfortably while also trying to figure out what is going on.

I remember he liked a girl that also disappeared.

Yes! That's the one.

Thank you!