Water: I've only done water about once or twice, but my general trick is to outline the edges with white/almost white and darken the water the further it is from land. Not sure how to add transparency yet without making it look off.
Rocks: I kinda cheat by just coloring in whole rocks then alpha locking and shading it to look kinda like a rock. It works for my style, but falls apart if you want something more realistic.
Grass: I color multiple layers of green and just start adding brush strokes on top and on the layer itself to kinda get the effect. Takes a while, but the result isn't too shabby.
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