Kyoto is full of small ponds. Some are dry, some are filled to the brim, some have lots of life in them, some are barren.
When I asked people what the ponds are good for I only got blank looks in return. They either didn’t seem to know that there are ponds all around or I was just not making myself very clear. Anyway!
I know that Tokyo at least has huge problems with rainwater because it is nearly completely covered in concrete and the water has nowhere to go. So they built enormous subterrenean caverns where the water is collected. My guess is that these ponds serve that purpose for Kyoto.