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When I use the merge tool on this polygon mesh, I end up with a multipart polygon with large gaps.

Before this, I was getting an error when trying to run a merge or dissolve because of "Polygons with overlapping Z values", so I exported a copy of the feature class without Z values to run the merge on.

example1

example2

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    Do you mind to specify the source of that mesh please? – FelixIP Sep 5 at 3:56
  • @felixIP it was the results of a flood model supplied to me by a consultant – JGIS Sep 5 at 4:20
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I am assuming that what you see is the result of invalid geometries inserted by whatever software created your "polygon mesh".

f you try to compute area, then I expect that you will see negative results for some of the polygons.

Using the Repair Geometry tool will fix it.

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