Corey:
In most states today, you could not build a green near a creek as at Augusta National or Merion or many old northeastern courses, because of water-quality issues. It's not a blanket rule, I was very surprised to find out what we could do in Montana, where they are used to clearing large acreages of land right up to natural water features.
The rules changed in the seventies. I was very surprised to recognize years ago that Mr. Jones' famous 13th hole at The Dunes is anything but a natural lake line ... they filled well out over a peat bog in order to get the edges of the water hazard just so, and no one cared. (Part of the fairway might be flagged as a wetland today if they stopped mowing it for a while.)
Ian Andrew noted an example of what you asked for a couple of months ago re: Cape Breton Highlands, but the reason they didn't go for the back tee with a stream crossing was the cost of the bridge, not environmental constraints -- and that course is on the fringe of a national park!