Hi Mike,
I sort of agree with John I that your nose will tell you, I honestly probably wouldn't use the water just to be safe unless I absolutely needed to use it. That being said, your post reminded me of something I saw awhile back about a couple turning there old pool into a kind of
aquaculture greenhouse.
http://www.homedesignfind.com/green/turn-your-foreclosed-swimming-pool-into-a-permaculture-fish-farm/
That was the best link I could find for it although I thought I found it before on a different site.
If it was me I might try and turn it into an Oehler style greenhouse by covering the top with a green house cover or hoop house whatever your budget will allow and then constructing an elevated bed system inside of the pool itself. The craziest version of which might be, a large scaffolding inside the pool made of either metal or water resistant wood and then fill the whole deep end with an aquaculture and above that have the scaffolding support raised beds. Would be a lot of work but probably really cool in the end. If you do decide to turn it into a cistern that is going to be one giant cistern

.
Anyhow good luck sounds like it will be a fun project.
Daniel