I seem to have read something somewhere where during low water that some people have buried stumps upside down in the banks, sometimes with cables and cement blocks attached to hold them until mother nature takes over. This has more of an ability to catch silt and promote fish habitat and then some old erosion methods of "armoring" the sides with cement etc., which is probably now illegal anyway.
Oh, and you can have all of my stumps for free, but you have to travel to Washington. I can haul you one small one tied to the back of my motorhome, I'd love an excuse to go back to the old homestead outside Rocky Comfort. Geez, that's what I should name my property here in Washington, ROCKY COMFORT. (glacier left me a goldmine in worthless rocks)
If you have found a fisheries or DNR person that you can deal with and wants to help solve the problem in different ways, you're half the way there.
My dealings with state agencies have been for the most part about as fun and fruitful as getting stuck in a quag.
For some reason, our state has the policy that if YOU do something, no matter how minor that causes silt, no matter HOW minor to hit the water YOU should be stomped on.
OK, fair enough, but if mother nature causes a slide that dumps tons and tons into the water, no problem, it's N A T U R A L, that's OK.
The catch to this is that when you see something you KNOW is going to happen, erosion wise, and approach them with the potential, and possible solutions to PREVENTING IT, they don't seem to be interested.
Talk about locking the barn door after the mud falls in the bay, they just sit and look at the open gate and let the horse run out. (oops mixing metaphors!)
I've had a couple of geologists spend half a day with me on some property I have and have learned a lot. That might be one thing to do before proceeding further. If you have in hand suggestions from people who should know it will help you if you get tangled with the state.
Some countys/states (all?) operate in a way that requires them to not grant any permits for anyone that actually asks, but don't do anything about anything that people are doing WITHOUT permits.
Maybe you could see what permits are necessary to build a "FENCE".
Put your fence inbound a little ways from the problem. Your fence posts should sit on a block of concrete about 4 feet by 4 feet, and your posts should be about 4 feet apart. You aren't doing ANYTHING to the shoreline, you are building a FENCE. Sure it will erode up to your fence, but will stop there. I know this may sound silly, but things like this have been done. One fire department in this state had a comment on their website about the current phony "smog" bans on fires in certain areas PERMANENTLY when in some cases people have no neighbors and have never been in a carbon monoxide "non attainment" area.
The website talks about the legality of "recreational" fires.
Apparently you can have a recreational fire if it is intended as a recreational fire. If your intent is to dispose of land clearing brush it is illegal. The website says that the intent of the fire determines it's legality.
Kind of like your problem. If your intent is to build a fence, it's OK, if your intent is to do ANYTHING to the creek...NO WAY.
In my area almost all of the "creeks" have been restricted by the fisheries department. This includes "creeks" that are only creeks along the road when it rains, and go away when it stops raining.
It's NOT OK to do anything to your ditch without all kinds of permits (routinely ignored). However, it is of course OK to let the fluids from cars run into the ditch. The county has a heck of time with about a third of it's drainage ditches from these restrictions. I often wonder if people that write some of these ordinances have even seen a fish or seen where fish live. ,
Good luck with your project.