An additional note about the pump and intake...
Most of the labelling is peeling off the pump, but I can just make out that the pump is RS ("Replacement Series") 750 by Hayward, model RS750CA, 0.75 HP, 1.32 SF, 0.99 THP. (To save another newbie the same search I just did, that's: horse power x service factor = total horse power.)

The intake from the pond's lower pool is equally difficult to see, but for different reasons. Here's a photo I was able to take after the water settled somewhat. The intake is approx 8" off the bottom.

Hey it sounds like your getting things moving. Is the pools done with liner or concrete? It is a relief that there was not sand media in the filter. I'm thinking that was some sort of bead filter. I'm all about filtration, I still believe you may need to add something. Filter mats will polish the water. You will need to keep an eye on the bottom pond since you don't have a skimmer. I can see that intake valve getting clogged quickly. I was wondering if you could wrap a filter matt around the intake. The only thing is I would be worried about burning up your pump. It would have to be something that you could get off easy to clean it. If you don't want to do a DIY filter, and you have the room. Look into Osaka filters. You would be able to hook it up just before the Triton. They are kind of bulky though.
About the fish, kinda funny, remember if you add koi. They are naturally a river fish. No matter what pool you put them in, they will find their way to the bottom.

Craig

Hi, Craig. The pond is fully concrete lined. There was a leak several years ago and the pond was drained and patched then. I've found a few cracks with plant roots creeping in, which is one of the reasons we've decided to drain the pond. None of the cracks are big enough to leak, but why wait until they are?

I agree the skimmer is an issue, particularly with the landscaping. Another of the big projects while the pond is dry will be to cut back or remove much of the most problematic plants. But that's a temporary solution. Can you recommend a floating skimmer, or a skimmer type that can be added on? (Option two is to ask the swimming pool guy to add the pond to his weekly skim.)

I had the same thought about that intake as you. In fact, I couldn't believe it wasn't already clogged when I saw the vast amount of mulm and string algae in the pond before I started cleaning. (I should have taken better "before" pictures, but we can summarize with: gross.) Given the long running with little maintenance, I speculate the inside of the T is filled with media to act as a primary filter on the system. When the pond is dry, I'll check it out. (Side note: The white haze in the photo of the intake in the post above is sunlight reflecting off the water surface. The pond water is a crystal-clear view into the brown mucky bottom.)

Here's a question for the experienced ponders: Despite the neglect, this pond has had clear water (when the mulm isn't disturbed and settles out), which leads me to believe there's some wonderfully beneficial bacteria/microbes/good guys living somewhere in the filter system. When I drain this pond for rehab, it will be dry for approximately two weeks. Should I try to save good-guy-infested media somehow, to re-seed the pond? Is there any effective way to do that?

Thanks!

Here is a link that might be useful: More details about the whole pond and the project

Hey Oscar
I have seen floating skimmers, however I've never used them. You can try one to help, but I don't believe it will work as well as one designed into the pond. As far as bacteria, first I think you water is so clear because of your bog filtration, plant root systems does wonders. I would think that you have a good colonization in the Triton of bacteria. Shutting the pond down for a while wont hurt. In fact I save my media all winter to jump start my pond in the spring.