When we moved into our house (in New England) there was this unheated swimming pool surrounded by tall trees. That didn't make much sense so I made it into a pond instead. It's about 24' diameter, circular, 4-4.5' deep. Something like 10000-12000 gallons. I put in 9 koi and now it's pretty hard to tell but maybe I have 60? Ranging in size from 1-8" in length. There is also a variable population of frogs and salamanders. (The frogs lived in the pool even when it was a pool. The only thing that bothered them was when we splashed around too much.)
There are two filters. There's a 3x6' gravel bed running a flood/drain cycle, fed by a 2600 gph submersible pump on the bottom of the pond, which has plants growing in it. I built this last year and only filled it with gravel a couple months ago (which added some sediment). There's also a waterfall filter (rated for a 5000 gallon pond) fed from a 4700 gph pump via the skimmer. That's been running for maybe 3 years now. At one point I had the skimmer feeding into the gravel bed and then the gravel bed feeding to the waterfall, but that resulted in variable flow rates which made it hard to adjust the flood/drain cycle (which is using an autosiphon) so I separated them.
On the plant side of things, there are four floating baskets with water hyacinths (based on https://www.gardenpondforum.com/threads/floating-planter-rings.2581/ ), three water lilies, pickerel reeds, and gamecock irises, plus I just started a half dozen each of tomatoes, lettuce, and basil in the gravel bed. All of which seem to be doing well.
I was hoping once I had the gravel bed running, especially with plants in it, that it would help the clarity. But... shortly after that was set up, we had a huge outbreak of gypsy moth caterpillars who completely stripped one of the larger oak trees over the pond. So, the entire canopy of the tree got chopped up into little bits or converted to caterpillar poop, and most of it dropped in the pond. It was clogging up the skimmer so badly I had to shut it off for cleaning twice a day. Last week, after there were basically no leaves left on that tree (and others), the caterpillars suffered a massive die-off and that is over now. So... things are running properly again, but there's probably still an excess of organic matter. Clarity was not great before this happened, and it's worse now.
Clarity... the water is pretty dark and visibility is less than 1'. There's a fair amount of particulate stuff in the water. I've tried adding a filter at the skimmer, but they clog up too fast (hours). Also, algae. Fish seem happy enough, though I did lose one during the caterpillar issues. I feed them daily.
I expect oxygen is good due to the waterfall and plants. An API test strip tells me nitrites and nitrates are around 0, pH around 7 at noon, GH General Hardness ppm (mg/L) 30, KH Carbonate Hardness ppm (mg/L) 40. (Tap water here is GH 80, KH 180.) I haven't added anything.
Given the volume, it's not generally practical to do large water changes. I've been dumping smaller amounts from the gravel bed after each rain, to get out some sediment, but that's probably <1% water change. If it was merited, I could do more but not on a regular basis.
So... mostly I am looking for advice on the clarity (although, since I've been making it up as I go, I'll gladly take other advice too). Is this something that is likely to clear up now that the other organic inputs have stopped? Am I short on filtration (maybe mechanical), and if so, what to add? Chemistry issues that need attention? I am willing to add filters and such (and I'm using quick connect unions so it would not be too difficult to do so), but since I want to use the gravel bed for aquaponics, I have to be careful about chemicals.
Picture attached.

There are two filters. There's a 3x6' gravel bed running a flood/drain cycle, fed by a 2600 gph submersible pump on the bottom of the pond, which has plants growing in it. I built this last year and only filled it with gravel a couple months ago (which added some sediment). There's also a waterfall filter (rated for a 5000 gallon pond) fed from a 4700 gph pump via the skimmer. That's been running for maybe 3 years now. At one point I had the skimmer feeding into the gravel bed and then the gravel bed feeding to the waterfall, but that resulted in variable flow rates which made it hard to adjust the flood/drain cycle (which is using an autosiphon) so I separated them.
On the plant side of things, there are four floating baskets with water hyacinths (based on https://www.gardenpondforum.com/threads/floating-planter-rings.2581/ ), three water lilies, pickerel reeds, and gamecock irises, plus I just started a half dozen each of tomatoes, lettuce, and basil in the gravel bed. All of which seem to be doing well.
I was hoping once I had the gravel bed running, especially with plants in it, that it would help the clarity. But... shortly after that was set up, we had a huge outbreak of gypsy moth caterpillars who completely stripped one of the larger oak trees over the pond. So, the entire canopy of the tree got chopped up into little bits or converted to caterpillar poop, and most of it dropped in the pond. It was clogging up the skimmer so badly I had to shut it off for cleaning twice a day. Last week, after there were basically no leaves left on that tree (and others), the caterpillars suffered a massive die-off and that is over now. So... things are running properly again, but there's probably still an excess of organic matter. Clarity was not great before this happened, and it's worse now.
Clarity... the water is pretty dark and visibility is less than 1'. There's a fair amount of particulate stuff in the water. I've tried adding a filter at the skimmer, but they clog up too fast (hours). Also, algae. Fish seem happy enough, though I did lose one during the caterpillar issues. I feed them daily.
I expect oxygen is good due to the waterfall and plants. An API test strip tells me nitrites and nitrates are around 0, pH around 7 at noon, GH General Hardness ppm (mg/L) 30, KH Carbonate Hardness ppm (mg/L) 40. (Tap water here is GH 80, KH 180.) I haven't added anything.
Given the volume, it's not generally practical to do large water changes. I've been dumping smaller amounts from the gravel bed after each rain, to get out some sediment, but that's probably <1% water change. If it was merited, I could do more but not on a regular basis.
So... mostly I am looking for advice on the clarity (although, since I've been making it up as I go, I'll gladly take other advice too). Is this something that is likely to clear up now that the other organic inputs have stopped? Am I short on filtration (maybe mechanical), and if so, what to add? Chemistry issues that need attention? I am willing to add filters and such (and I'm using quick connect unions so it would not be too difficult to do so), but since I want to use the gravel bed for aquaponics, I have to be careful about chemicals.
Picture attached.
