Yikes….I say doing it that way is far too much hard work! Creating a river bed by carving directly into a piece of MDF to me is too time consuming and you can get better results with additional materials.
I made a whole series of modular boards with 1/2" MDF as a baseboard. However, I glued sheets of pink insulation board to the top of the MDF and carved the river into THAT. The MDF layer ends up being the river bed/water level layer upon which you put your water effects, paint, etc.
The other problem with using a piece of MDF board that large as the actual terrain layer itself is that it is almost certain to warp. Also a piece that big will probably have a curve to it any way due to its weight. Another disadvantage to it is that you have to use a resin-type water product to create the actual water, which involves the whole ordeal of sealing off the ends of the river beds and pouring several layers of resin.
If you use my technique, the MDF already creates your "water level", all you have to do is paint it and then apply something like a gloss Mod Podge sealer or simply paint with a layer of gloss varnish over it.
The other problem I can see with trying to dremel and route right into 1/2" MDF is that you're leaving an awful thin layer of MDF underneath by the time you make your river channel deep enough.
Here's what I did with the 1/2" MDF and insulation foam. The layer of foam allows you to do MANY more things, like carve shorelines, etc.
Here's some pics of what I did:
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Here's the same technique with which I made a couple different coastal boards:
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