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Im a landscape architecture student. From my limited experience I would say 3:1 max slopes on the banks if possible to deter erosion, avoid using rip-rap or stone on banks to encourage habitat, and try to think about blurring the line if you will between land and water and what happens during a flood event and a drought event. As far as high and low water, how can that encourage habitat and different types of plants and animals?
I'm not sure on sealing or capping the earth, I suppose it would largely depend on the soil composition whether its a clay or sand, etc.
In laying out the routing for your water courses you should try as much as possible to follow the existing contours, ie "natural lay of the land," and perhaps avoid putting water on ridges and hill tops. The streams should flow at a minimum of 1-2% grade (maybe more per agla's comments) which is perceptually flat, ie 2'-4' of drop for every 50' in horizontal distance.
Those are just a few things I'd consider.
hope it helps..
-n
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