Take a sample to your local pet/aquarium store and have them check it or buy test kits to check nitrite, nitrate, ammonium, etc levels.
Obviously you’re not going to use bottled water for your pond!
How many gallons is your pond? And with the filter not running your water went clear … also because you weren’t adding new water. Do you have koi that are stirring up the bottom, causing all the gunk to circulate to the filter? Assume your filter is maybe on a skimmer or towards the surface? Or are you talking about the cage on a pump that is towards the bottom of your pond? If it’s on a pump cage that is on the bottom, move the pump up off of the bottom, put it in a milk crate. Let the algae settle to the bottom.
Another suggestion if you have koi that are stirring the bottom, add smooth river rocks to the bottom. They will gather the green algae/beneficial bacteria that needs to be on all surfaces to help break down nutrients in the water. The idea is two-fold. The rocks have more surface area than liner, and the koi won’t stir up the rocks on the bottom. I never had rocks in my IL ponds. Koi pond was 95% of the time murky. Goldfish pond was always clear. (Goldfish tend to not root on the bottom.) Now we have rocks and the water has been crystal clear since pond was built last year in July.
Another suggestion is to add beneficial bacteria to your pond to help boost the colony. I found a product that uses only 1/4 cup for 5-10,000 gallon ponds!!! I add it weekly. It’s called Ultra
Clear Clarifier. Besides the natural beneficial bacteria, I don’t add any chemicals to my pond.
Hope these suggestions will help you!