Matrix metering on the D7000 is very good. You need to be able to dial in positive or negative exposure compensation - depending on the scene, but there is no compelling need to do a lot of spot metering and complex exposure management for the images in your link.
The key to metering is to use your highlights display (blinkies) and your histograms. I find the histograms are difficult to use for small overexposed areas, so the blinking highlights are more useful. Just dial in exposure compensation so you eliminate most or all of the blinking highlights.
I would certainly use a circular polarizer - you have reflections on water, off foliage, and in the sky. A ND filter is good for waterfalls, but nothing beats even light from overcast or rainy conditions. For sunny rivers, don't use the CP to kill all reflections. Instead, adjust the CP to optimize the reflections in the water.
If you are using Nikon View or Capture for post processing, you probably can get some help by using ADL Low. ADL Normal and beyond adjusts your exposure as well, and I try to avoid exposure adjustments.
You can create a HDR image from multiple shots - essentially bracketing in two stop intervals. It's done in software as long as you have the images to use.
Keep in mind that there are specific things that can influence the exposure even with Matrix metering. If you have a lot of bright sky in the frame, the camera will try to make the exposure darker. If you have a lot of dark, polarized water or bright green foliage, the camera will try to make the scene brighter - more toward neutral tone.
One thing you have not mentioned is white balance. I find auto WB tends to neutralize the great color in a scene, so you might want to use Daylight WB. Of course, that's if you are using software that will honor the camera settings like View or Capture.