Thank you, you're right, the spa was mostly aesthetic because of the spillover. My mother-in-law just likes the pool to look nice which is why we didn't cover it over winter. I'm sure there is definitely dirt in the water when it comes back in, crazy though, I thought there would be mud or some kind of color when the water was sent into the spa... but it appears clear.If you can sufficiently get chlorine into that water, sure, but that is hard when you are pulling in dirt with it.
I would think for at least the summer, it would be wise to isolate the spa. Most folks do not like to use it in the summer, and you do not have a heater, so not sure you want to use it in the winter either.
Maybe years of this has caused there to only be hard rock remaining in the hole. I'm going to get the water in the hole tested for microbes and metals make my decision from there. Thanks again for being so helpful. I plan to stick around the forum and learn and hopefully be able to help someone else someday.