I have never seen any ill effects. For my personel stuff, I usually let it set up and then run the system for a week before draining the system to start it up. I let it run to make sure it does not leak, that would suck.
On a side note, make sure you have shut off valves where water leaves and enters the aquarium, just in case there is a leak. Would suck to have a plumbing leak and not be able to stop the water flow.