Water Bases were once constructed to accommodate more survivors and to preserve the biodiversity of flora and fauna from before the natural disaster, so whether it was the Plantation Garden or the breeding rooms, they only occupied a small portion of the base.
It wasn't that they didn't want to preserve more species of plants and animals, it was just that when the Water Base was being constructed, allocating more space for flora and fauna meant reducing the living space necessary for survivors.
To give a simpler example, rearing one more cow might mean the loss of boarding eligibility for one or two people.
Now, with the advent of the Enhancement Scroll, the base had expanded to about three times its size. Although it wasn't an overall enlargement, just an expansion according to the base's square footage, it was still a significant area.