The rivers are definitely a problem. Rivers seldom split as they flow downstream. And when I say seldom, I mean so infrequently that if you depict one doing so, you'd better have a darned good explanation for it prepared ahead of time. Usually it can only happen with human intervention—flood control or irrigation or canals. Stylistically, they don't really look like they're carrying water across the landscape. They look like damp spots. Assuming the rivers are on a separate layer, ctrl-click that layer to select them, then switch to whichever layer holds your land texture, and hit the Mask button at the bottom of the layers palette. This will carve a space in the texture for the rivers to sit in. Then raise the opacity of the river quite a bit so they are more visible.

Now to get the look of your mangrove swamp, make a new Hue and Saturation Adjustment Layer on top of your layer stack. I'd suggest turning down the saturation a bit, and sliding the hue slightly toward the blue. Your entire image will change, but don't worry about that—we'll limit the scope of the adjustment in a few moments. Once you have a color in that basin that you like, select the Mask on your adjustment layer and fill it with black. Then use a soft round brush to paint white in the places where you want the adjustment layer to take effect.

Regarding your fuzzy selection problem, the tool won't automatically select black. On the right-hand side of the dialogue box, there are three eyedropper icons. Click the left-most one, then click in a dark area on your image. Now you can adjust the fuzziness, and you should get a selection that starts in the darkest areas and creeps toward the white as you adjust the slider.

No time to talk about mountain placement in any depth, but from a quick look, it doesn't appear to be a problem to me. It does look like maybe there was an asteroid impact, with that ring of mountains surrounding a huge bay/sea.