Check for geometry errors in the dataset before running the tool using a polygon layer as the zonal input
Geometry errors within the polygon dataset cause the tool to return erroneous results. To identify geometry errors within the dataset, run the Check Geometry tool in ArcMap. If the data is corrupted, run the Repair Geometry tool. For more information of identifying and repairing datasets, refer to Checking and repairing geometries.
Install 64-bit background processing and allow the tool to run in the background
Background geoprocessing uses the 64-bit mode of the tool and utilizes more memory to complete the process. To enable background processing, in ArcMap, navigate to the main menu, and click Geoprocessing > Geoprocessing Options. Check the Enable option in Background Processing. For more information, refer to the following ArcGIS Web Help page: Background Geoprocessing (64-bit).
Use parallel processing
Use the Parallel Processing Factor to utilize all cores of the computer to boost operation performance. For more information on the Parallel Processing Factor, refer to the following ArcGIS Web Help page: Parallel Processing Factor (Environment setting).
Specify the raster resolution as the cell size for Raster Analysis in the environment settings
When the raster cell size is larger than the zonal polygons, the Zonal Statistics as Table tool returns "ERROR 999999: Error executing function", and the zonal analysis is interrupted. To prevent the error, select a suitable output cell size for the resulting raster. The cell size ranges for raster can be calculated using the Calculate Cell Size Ranges tool. To specify the cell size, in ArcMap, go to Geoprocessing > Environments > Raster Analysis, and select Maximum of Inputs from the drop-down list for Cell Size. For more information on selecting a suitable cell size, refer to the following ArcGIS Blog: Choosing an appropriate cell size when interpolating raster data.
Calculate the statistics for raster datasets before running the tool
Running the Zonal Statistics as Table tool for raster datasets without statistics data returns the following error message:
ERROR 010213: Error in reading raster [raster file directory].
Ensure that the Zone field does contain Null values
Null values in the Zone field cause the tool to fail and return "ERROR 999999". To solve the error, copy and paste the non-null field values into a new field, and delete the old field that contains only null values. Run the Zonal Statistics as Table tool for the new field. For more information on copying field values into another field, refer to Copying and pasting records in a table.