I think I've got it, actually, but I will also try those settings out this evening. I've got an evening class in about half an hour, but I thought I'd post the updated version along with my babblings. The water level in the following picture is about 10, and it seemed to work.
Mowhawk, I think I saved over the file where I was having the problem, although I have a lot of different save points so I may be able to find it if you still want to see it.

Babbles written during tweakage process:
Mowhawk, I wasn't quite sure what to do about the yellow saturation; did you mean the color variation isn't enough? Or that it should be a paler shade?
I lifted the dune grass, but now it kind of takes over the image, so I think I'll lower the scale a bit. Maybe move it closer to the water... or the water closer to the grass...
As for the stone size, have I lowered it enough, I'm going to decrease the scale more. It looked much improved in the cropped section I compared, but seeing the full picture, it doesn't seem enough. Also, maybe I raised the water transparency too much? o_o More tweaks to come
Again, thank you all so much, your help means a lot to me!