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I used grassgis delineated watersheds in a large area. After vectorizing the watershed raster, I ended up with a lot of tiny watersheds.

"Dissolve" did help a bit, but there are about 1200 watersheds I would like to eliminate. The "eliminate" tool in ArcGIS could do the job most of the time, while wrong combinings still occur.The following pic is not exactly the wrong combining, but looks like it.

I need to eliminate some small watersheds to have most of the watersheds around 100 sq km. And the eliminated watershed would be combined to an adjacent one which belongs to the same drainage system.

Are there any tool can combine those small watershed wiser?
Two highlight watersheds are combined

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    In your picture it's not clear what should be eliminated, why and when. What is the criteria for eliminating a watershed? Is there a threshold area?
    – GISGe
    Dec 1, 2016 at 9:47
  • How do you determine which watersheds should be combined? Is it enough that they are adjacent, or do they also have lead the water through each other (e.g part of the same drainage system)?
    – Martin
    Dec 1, 2016 at 10:20
  • @GISGe Thx for your comment, I forgot to mention that I need watershed area about 100 sq km. The small, highlighted one is less than 10 sq km.
    – BBR
    Dec 4, 2016 at 1:18
  • Hey @Martin Thx for your comment! The watersheds should be in one drainage system.
    – BBR
    Dec 4, 2016 at 1:20

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Perhaps re-run your watershed analysis. Typically watersheds are created one of two ways, from a pour point or from a cell count threshold. If you know the cells size of your DEM, you can figure out how many cells you need for 100 km2 and set your contributing cell threshold to this number. I typically will run the analysis a few times with smaller thresholds and create multiple watershed layers which I can then combine as I would like.

If you aren't able to rerun the analysis there might be some relevant attributes, or if you have access to the other watershed related layers (flow direction, flow accumulation) you might be able to use these as inputs to meaningfully merge smaller polygons.

Rerunning the watersheds at a few scales is your best bet IMO. Your objective of creating equally sized watersheds makes me think you might want to play with these tools a little bit anyways... just to wrap you head around the pieces.

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