I am slowly building my own City in a spare room I have. I was contemplating putting in real water in certain places for boats, fountains, pools, etc. Does anyone know if being in water long-term does any damage to Lego pieces? (Btw I would only use bottled water)

Not sure... theoretically it could cause stains along the waterline like in real life but lacking sediment due to the water being sourced from bottles I'm not sure. There are several cool alternatives to real water though, especially since when in small quantities the water won't look like that familiar bluish clear we all know. You could use unattached 1x1 rounds like this:

Or you can use transblue tiles:

Or you can use clear plates on top of a blue plate (I don't recommend the ordinary blue baseplate, it doesn't look as good)

Lastly, you could use SNOT technique to create a solid and flat water surface:

That's funny. I contemplated using a large fish tank on the end of a layout to make a harbor/ diver scene. I would also have fish for the kids.

Use distilled water. It's 100% free of minerals that cause the staining. They sell it by the gallon at the grocery store. That being said after awhile things could eventually start growing in the water. You would have to change it,regularly and/or add vinegar to kill anything. I would do a test first.

Bricks would eventually stain.....and algae/bacteria/micro would grow. If it was a clean room....with di water...and a microbial surfactant...that would work fine. Standing water would attract all the dust/hair/dead skin cells to make a film on the water...which throws off the PH...which will cause staining from the acid/base diffence of water vs. atmosphere. Standing water would then attract micro organisms....which would grow into a mess..not to mention the evaporation and constant filling.

Cliffs notes...hit the pab wall when they have trans blue. Hard. Big cups.

Bricks would eventually stain.....and algae/bacteria/micro would grow. If it was a clean room....with di water...and a microbial surfactant...that would work fine. Standing water would attract all the dust/hair/dead skin cells to make a film on the water...which throws off the PH...which will cause staining from the acid/base diffence of water vs. atmosphere. Standing water would then attract micro organisms....which would grow into a mess..not to mention the evaporation and constant filling.

Cliffs notes...hit the pab wall when they have trans blue. Hard. Big cups.

Exactly. 1x1 rounds in trans blue and light trans blue are quite common, as are 1x2 clear plates.

I had originally thought of the water staining and having to constantly recycle the water. I have decided to more or less cut out the water idea. Although I may still continue on my fountain idea. It would be one that would actually work. Also that would help with the standing water issue. I appreciate all of your help and good luck to you all in the future