I'd agree. The "muddy" look is best achieved by adding color to the "water" material.
This is the bottom of a pond I did recently, before I added "water."
I wanted a mostly-clear pond, but I added a bit of color to each pour. I used Envirotex for the water. I mixed about 2 ounces at a time, and put just a drop or so of acrylic paint in each batch. The actual depth of the whole stream is about a half-inch at most. I did this area in 3 pours.
Before you do this on your layout, I'd suggest mixing a few test batches of your "water" material with paint, to get an idea of how it's going to look.
It takes an iron man to play with a toy iron horse.
Your best bet would be to use a fill medium that you can muddy and make somewhat opaque. But, if you intend to cover a painted bed with clear gloss medium or epoxy, then use a plain brown, and add some black or white as you wish to darken or lighten it.
Hi Guys, Just about ready to color my stream bed. When done with the water want to have a muddy look.Was wondering what color would be the best to use. Will be using acrylic craft paint.Also in the middle of the stream will be a small waterfall . Let me know the best ways to make a waterfall . It will only be around 4 inches tall. Any advice would be appreciated. Thanks