You either have an "up flow" or you have "flow through". If the water is falling into the stream from the waterfall, you would build a flow through. But the waterfall would have to spill into the first level and then the wetland would be at the second level.
@Meyer Jordan can help here - I would be concerned that the planted portion of the stream would slow the water flow as the plants got bigger - you would have to be able to control how much water can come through the waterfall as the plants grow through the season, I'm guessing.
To have an up flow, you need to plumb the water to enter the "bog" from the bottom and get pushed up through the gravel and plant roots.
You can combine a waterfall box with a vegetation filter - that's commonly called a biofalls. The top of the waterfall box is open and can be planted and the waterfall flows out the weir at the front of the box. There's no gravel involved, but the principle is still the same.