You can quote me. I use enamel paints to tint Envirotex...or, to make it "muddy". I've done some areas on others' layouts by dripping the tan/brown in the pour before it cures, and, using a screwdriver or skewer, blend it to look like waste water coming out of a factory.
I can't speak for acrylics or lacquers (such as Floquil). All I know for sure is that enamels work GREAT.
However, I believe the "perfect" solution to adding "depth" to a river, pond or lake is to airbrush the bed (riverbed, lake-bed, etc.). The best practice is to go somewhere to a stream and take photos of it from different angles. If you can get a high angle, that will be your best example since we're looking at our N-scale scenery from high above usually.
Remember, and this is important, the vast majority of times, the water is NOT blue, or a shade of blue when seen from above. It's usually green, with the depths being a deep green-black. The shallower areas are lighter shades of green and the shorelines are a couple of shades darker than the dry dirt above the water-line (spit on dirt...it turns dark). Sometimes there are a lot of weeds in the water, and they are pretty obvious close to shore. You can "imply" them by painting smoothly squiggly "weeds" using a lighter shade of green...but, still blend them into the "depths".
Also remember how a river cuts into the banks. The outsides of the bends are where the channel is, and where the bank is the steepest, so don't always run your channel down the middle. Often, there'll be a sandbank on the insides of sharp river curves...which slowly fades into the channel.
After your riverbed is painted, dam up the ends where it runs off the layout (I just use masking tape), and look for any little holes by placing a bright lamp under your riverbed, then turn out out the rest of the lights. They'll show up as pinholes of light when viewed from above. Plug em up with modeling clay that's the appropriate color, because if you don't, the Envirotex will leak all over your floor...and I guarantee you, you don't want that!
Mix up some Envirotex (you don't want to do over a 1/4" layer) and pour it in the painted bed by holding it high and letting it "string" down onto the bed. Use long straws to blow on it to get the bubbles to come to the surface. You'll end up dribbling spit onto it. Don't worry, it won't effect how it sets up or looks.
Let it cure until it's hard, then mix up more batches until you've got the depth you want. Only pour 1/4" layers. You really don't need much more than 1/2" since your painted riverbed "implies" the depth.
You'll note that Envirotex will creep up into lots of detailed areas and over rocks, logs, branches, etc. Don't worry about that right now.
Now, after the resin has cured (a day or two) add Acrylic Gloss Medium with a medium sized round brush, and make the deep parts smooth, and the shallow parts have ripples. Refer to your photos to get the ripples right...there's a pattern to them.
If you want bigger rapids, you can apply thicker gloss medium (it comes in several thicknesses) or WS "Water Effects". You can also paint white-caps on the higher rapids using Titanium White Acrylic. Use a teeny brush for most of this. You want to keep them 1/160th scale.
You can also work the gloss medium into the shallow areas and add reeds, etc. to it.
If you want to get rid of the Envirotex "creep" on rocks, logs, etc., mix up some flat paint and paint those details where the resin has "crept".
This method will give you both depth and texture, and it works very well for me.
Here's a photo of a river I built for Art McCoid. Kelly Newton designed the modules, and did 90% of the work. I built the bridges, some of the grass and trees and did all the water.
Here's the Weber River on my old Wilhemina Pass module, and it's done with just gloss medium, and no Envirotex. It's got a perfectly flat "bed" made out of Foam-core, and the depth is simply implied by paint.
You'll note that the "blue" color is reflected skyboard, just like real water which reflects the blue sky. I didn't add any tinting to either of these. Personally, in my experience, tinting better implies muddy water than clear "blue" water.
Cheers!!
Bob Gilmore