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I have one polygon stored in a shapefile and an WFS Layer with a lot of Polygons. Is it possible to filter the WFS by the shapefile-polygon before the Download begins, in QGIS or ArcGIS? I just want to Download these polygons which are within the big area (.shp).

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It depends on two things.

The WFS has to be enabled for filter encodings. You need to check that first in the capabilities document.

The second limitation is only possible to use the bounding box of your shapefile. There is no upload and clip functionality for WFS.

You need to set the filter expression in the service parameters in ArcMap.

<Filter>
    <BBOX>
      <PropertyName>NAME</PropertyName>
        <Box%20srsName='EPSG:your_CRS'>
            <coordinates>your_bounding_box</coordinates>
        </Box>
    </BBOX>
</Filter>

In QGIS its a bit easier as you only need to input the bounding box coordinates when using the extension WFS 2.0 Client.

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