Welcome, Josh!
It appears to be Filamentous Algae (FA). And as I too am a newbie I also had the same problem in my 2 acre pond, followed by a fish-kill.
From my understanding, it's growing due to high nutrient levels to feed it as well as clear water allowing the sun to penetrate the bottom also allowing it to grow. This may be why you're seeing it in the shallow areas.
Possible Remedies?
You can use a pond dye but it may not help for the 3' or less depths.
You can treat it with Cutrine Plus (granular or spray) but then you have the issue of oxygen consumption as it decays, adding even more nutrients and possibly causing a O2 crash if you treat too much at a time.
Raking or scraping out as much as possible to prevent it from O2 consumption (it's great fertilizer!).
Find out where the nutrients are coming from i.e., runoff from fertilized lawns, fields, etc. It also looks like there's a lot of trees which add to the "muck" via leaves, etc.
Install an Aeration system which would be somewhat costly for a 5 acre pond.
Plant life will put out oxygen during daylight hours and consume it after dark with lowest oxygen levels just before sunup. Is there pond weeds, vegetation, etc., surrounding the pond? These will help consume oxygen leaving less for the FA.
So on top of fishnchips great questions;
How is the water clarity?
What is the age of the pond and how much or how deep is the "muck"?
Hopefully there will be others more qualified to chime in, the above is just from my experience and what I've learned from the great folks here on PB!
Read up and research, there's tons of great information here. And hopefully I'm not too far off on my assessment.
As with fishnchips, good luck Jim!
Water clarity currently is about 8 -10 inches.
I have no idea the age but I would guess 20+ years based on the age of some of the first residences although I don't know that it was constructed during the subdivision or the subdivision was planned around it
On the west end it backs up into a wooded area so leaf/ much buildup is deep over there. It is about 2' deep at normal levels but that third of the lake wAs dry late last summer.
There is runoff from an AG field that goes in as we'll as runoff from a couple highly manicured lAwns. The remainder of lawns are just mow and go
