not sure how the one you are talking about was done, But if I wanted to do it I would make the basic shape of the river I wanted, copy/duplicate it, align the two, place them in the ground where you want them, select one and use a boolean to knock out the shape from the ground, apply water texture desired to the one left...  maybe expand it 1-2% to make sure there is no weird voids...

just a thought....

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Hexagon, Carrara, Sculptris, and recently Sketchup.