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I am trying to create a contour map for a waterbody. It turns out that in several locations there is no data. I just don't want to use the missing values as zero in ArcGIS because it would create several other contours by interpolating actual value and the zero value. Can someone suggest to me any good way of handling N/A or no values in ArcGIS to create contour maps?

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If the NoData areas are tiny, this would be a form of "patching gaps": please see the discussion at (around 80% down the page). – whuber Feb 27 '13 at 14:30
When you say"create a contour map for a waterbody, are you talking about bathymetric contours?? – TsvGis May 26 '13 at 6:39

Use the Contour with Barriers tool in ArcGIS for this. The missing areas can be barriers. See this blog post for more info.

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