I always associate that dark brown stained water that is clear with humic acid conditions in a pond. I used to fish a lot of "forest" ponds and they were always that color. (But I didn't have a test kit and wasn't a PB member then!)
Humic acid forms due to the decomposition of organic matter. I think a Kansas pond in June should have a green tint. I suspect your algal bloom has peaked and then began dying off. Also, the terrestrial plants on your pond bottom that were above the water surface are now dying after being submerged. Finally, your Pondweed that was in shallow, clear water may also be experiencing a die off when your pond went to full pool and muddy water after the rains.
I think you had long term plans to add some aeration to this pond? If so, now might be a good time to expedite that plan.
P.S. If I am correct about the humic acid conditions, then you might want to invest in a cheap pH testing kit. The change from your usual conditions to this condition would probably be easily observed on your test strips.
