The netCDF file does not contain a variable that is valid for the tool or the variables are in a group.
Review the content of the netCDF file to see if a valid variable exists. If the file does not contain a valid variable, the file is not a suitable input for the tool. If you are encountering this message in the Make NetCDF Raster Layer tool with variables in a group, use the Make Multidimensional Raster Layer tool instead. If you are encountering this message in the Make NetCDF Feature Layer or Make NetCDF Table View tool with variables in a group, you can extract the variable and save it to a new netCDF file without a group and use the new file as the input.