As you have noted, for some reason ArcGIS Desktop (ArcMap) cannot properly interpret the coordinate system from this file. However, ArcGIS Pro is able to interpret and georeference the 'shtfl' variable in this file. This is possible because the file contains CF-compliant metadata (CF Conventions Home Page ), with a coordinate system variable ("Lambert_Conformal") and the 'shtfl' variable contains a "grid_mapping" attribute that points to the coordinate system variable. If you would like to visualize the 2D latitude and longitude variables ("lat" and "lon", respectively), you can simply add a variable attribute 'grid_mapping = "Lambert_Conformal"' to each variable. You can do this easily with the NetCDF Operators (NCO, NCO Homepage ) command-line tool 'ncatted', specifying to append ("a") the character ("c") attribute named "grid_mapping_name" to the "lat" and "lon" variables in an existing file. Example below: > C:\nco\ncatted.exe -a grid_mapping_name,lat,a,c,"Lambert_Conformal" .\shtfl.2000.nc > C:\nco\ncatted.exe -a grid_mapping_name,lon,a,c,"Lambert_Conformal" .\shtfl.2000.nc Once this is completed, you will be able to bring those variables into ArcGIS Pro using the Make NetCDF Raster Layer tool, just as you did with the 'shtfl' variable.
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