Those are nice shots. I agree, the blues in the water are strong. However, the same strong blues make for a very nice looking sky.
So, at this point you have some options, here are a couple I'd suggest.
1) Say "It's HDR, and I like the look, the blues stay!" (Simple and easy)
2) Take the photo into your favorite editor and tone down the blues in the water. I'd probably do that by creating a duplicate layer, de-saturating it a bit, and then use a layer mask to paint in the less saturated water. Of course there are lots of ways to do it, that's just one option. In this particular image, I'd only try and do the waterfall, there's so much brush and leaves in the rest of the shot it's going to be very difficult to layer. But you could do the falls fairly easily and I suspect that would help with the blue water look.