How Can I Restore Flow and Health to a Creek Full of Decaying Matter?

So here’s pictures of my grandparents creek. It has been stagnant and full of decaying matter / nasty thick mud since they bought the place 40 years ago. I would like to somehow restore the creek as it’s not like other in the area, many on the other side of my hill flow fast and don’t stagnate like mine and it’s the only one in the area I’ve seen like it.

Here’s a general overview of my creek:

So my creek comes out of a spring house and flows into an old pond area, (which is picture 1), and then it flows down in the rest of the pictures for several hundred feet before it hits a drop off (picture 5) and the thick mud and debris are gone and it picks up speed and then eventually hits my cave (last picture) and goes underground from which it comes out in my ravine. It also does not flow to the cave all year round, it’ll sort of stagnate and dry up in the summer and fall, turning into a bog.

So if anyone has any advice or recommendations that would be great as I’d love for this creek to be restored and functioning again like other creeks in my area.