Pond Makeover planning

30x40' pond needs to be dredged and I am researching options for the depth, reshaping and natural beauty of it.  I plan to have a few ducks/Muscovy and some fish. Looking for a natural habitat that's closed loop. Hopefully a system that will be clean enough to swim in.

Should I build in a shallow ledge for nesting and shallow rooted plants?  
How deep should it be at the deepest part?  I was thinking 6-9'.  Living in chilly zone 3-4.
Will the ducks seal the unlined pond after it's scraped by an excavator?
What perennial plants will be best for cleaning the water and making happy ducks and fish?  There are cattails and some grass now.
Thinking about adding some swales under the high backside of the pond where it slopes down.  Facing a treed south and a lot of wind. Tips?
It has a bunch of largish gravel on all sides that was brought in for some reason.  Any ideas on why, whether to keep that or remove it?
What are some things to do with all that rich rotting material that will be rescued from the pond dredging?  It may have a bunch of gravel in it.
Will ducks head to the river to be swept away or be content with their pond?
Would 3 ducks and future ducklings be a good number for this size pond?

Thanks for reading and adding your experience.  This is my very first post here.

Congratulations on your first post. Good job. I have added it to the forum ponds, so you have a better chance in getting your answers.
Keep us posted on the progress, it sounds like a great project.

Hi Michelle,
Welcome to Permies.

I don't have much pond experience, but I noticed you mentioned wanting it clean enough to swim in. It made me think of this other thread where ducks were getting into a natural swimming pool... and people did not seem to like sharing the same water as messy ducks. Just something to think about.

https://permies.com/t/257311/persuade-ducks-hang-pond-natural#2418787

Best is in layers. 10 inch for a while, then 15 for a while, then 20, Imaginary depth levels i used, i forgo,t sorry, Different plants like differing debts to establish themselves in.
Sludge is rich in compost. I'd use it for pumpkins the first year, Never mind the gravel.
Plant reeds or yellow flag, they clean and pump oxygen into mud.
Some fish are not too bad, If people want to put Koi in , shoot them at sight (joke). recipe for disaster, All those carp like mudturners are, I got fish that keep the plants in check, but do not eat all, but i'm in europe. The plants keep the water oxygenated.
I've been to all and every pond/lake in the surrounding area to gather local waterplants and insect life and even microbes that come with it,
My pond is tiny, but i've build a natural swimming pond that was gorgious until the owner decided to safe a lot of fish that were drowning on a dried up lake in a hot year. Now they're a huge shoal and each and every shits as much as a small dog daily, Nobody wants to go in but he won't allow people to fish the poor fish...
These kind of projects go bad quickly with poor choices,
Can you send a picture please?