As to color ...
As to color, Marty's right, straight blue doesn't really look right for modeled water. However ...
I've found adding a bit of blue to the other colors I use for water helps - that is when the water is fairly clear and free of silt (more about silt-laden water later).
For the deepest areas, I will make them blue-black, midnight blue, if you will. Then I will take the dirt color along the banks, add just a few drops of blue-black, and then paint it along the shore. I blend in a bit more blue-black as the water gets deeper, until it blends completely into the blue-black of the deepest areas.
Don't add very much blue - it needs to have just enough blue that it looks like an ever-so-slighly bluish black.
Using a few drops of blue-black makes the shallows along the shore look wet (even when you can't see the reflected gloss), and contrasts nicely with the dry dirt color above the water line.
Regarding silt-laden water, depending on the level of silt in the water, you can pretty much throw the whole black/blue-black water coloration method out the window. Lightly silt-laden water can look anywhere from dark olive green to dark red-brown in the deep areas. Heavy silt-laden water has almost no sense of depths or shallows and is generally some shade of mud brown - from red mud to yellow mud, depending on the color of silt source.
Many Oregon streams and rivers have some amount of silt in them, so dark olive green to green blue in the depths actually looks correct. Notice the color of my North Umpqua River in the scene below - this is modeled from photographs of the river. The North Umpqua is snowbank-fed and has a distinctly blue-green silt coloration, so locals can quickly tell this is a model of the North Umpqua. The spring-fed South Umpqua silt creates a much more olive green color to the South fork:
And here's a photo of the actual North Umpqua river for comparison:
And here's the South Umpqua for comparison:
Of course, colors can shift in photos, but trust me, these two photos are a fairly accurate representation of the silt coloration of these two river forks - the South Umpqua River water is more yellow-green. By paying close attention to modeling river coloration, you can get an accurate model of water that even the locals will believe. The presence of silt in the water can give each body of water a unique coloration that's different from the generic black/blue-black approach for the deep areas.
