You should be able to draw in water by using the water tool.
But, it will flatten a very wide area around the water. I would use grass or sand or brick with the water tool that will outline the area that water will be, that way when you raise the land back up and smooth it and all you will know where the water stops.
If that doesn't work, then you will need to go to Advance and turn on the water limits - then go over the area with the flatten tool - it should remove the water, even though you will still have a dent from using the valley tool.
One you do that plateau tool the landscape, then using your water cliff tile with a contrasting texture, draw out your water larger than you want it. Turn off the enforce water and then go back with your valley and plateau tool lowering and then drawing out your river/stream.
What you might need to do is start fresh - meaning make a new map the exact same size as this one, setting the cliff height at 3, then copy and past that over this - it will reset the whole map to where there was no water.
Yes it can be a pain at time, and why it sometimes fails is beyond me.