Quite a transformation through the three pictures. Nice pond and setting.
There are some old threads here on PBF where guys have done extensive work to solve sediment problems just like you are trying to do. Maybe some of those people will see this or you can sift through the old posts and find them.
I've created a sediment pond ahead of my main pond, but it was only completed this year and we have yet to have enough rain to see how effective it will be.
One suggestion would be in the area you are going to deepen the pools in the stream where the water enters. Anything you can do to slow the water down will help the sediment settle out. For example, if you could cause the creek to meander, with right hand turns, it would be much better than going straight through the pools. Rip-rap the corners so erosion does not happen on the banks where the water hits it. Create a longer, slower path for the water to follow.
The other suggestion is to, best you can, keep the area designated for sediment either 1. very large so it rarely has to be cleaned out, or 2. built in such a way that it is easily and relatively inexpensively cleaned out with a backhoe or other machine.
That is all I got. Others will come along with more ideas.
