Perhaps you have take a piece of paper and shade draw the areas you want deep, or shade them in a bitmap program like PhotoShop, or Mypaint, or Gimp, and then export it as a .Png
…and then use the Heightfield command, setting the perimeter, height and resolution to create a nurb patch that describes the bottom.
Then you can insert a solid into it to create the water, embellish it with some trees, rocks, plants, and logs Walla!
Alternatively, you could do it manually by creating create a plane, rebuild it adding some nodes, and just move them around manually. Rhino has soft-select tools that might help.
Alternatively, you could download someone else’s swamp heightmap.
Often, if you try to cut the water volume with the land surface, the resultant fit will be a problem for most raytracers. It’s often better to just insert a block of water just below the top surface–and let the raytracer clip these objects wherever it sees fit. You can extrude and bend shapes to make a waterfall, and add alpha-blended textures to make splashes.
A plugin to distribute grass and cattail plants might help.
Oddly, in some computer games, the use height-fields made from real areas to simulate simulated fake ones : P