The threshold for subbasin areas is really a threshold on the area
required to form a stream, so it only directly affects outer subbasins -
ones in which streams start. You get small internal subbasins where
stream junctions occur close together.
QSWAT is an alternative to ArcSWAT, using QGIS instead of ArcGIS. It
has an option to automatically merge small subbasins with their
downstream subbasins, where you select 'small' in terms of either area
in hectares or percentage of mean subbasin size.
QSWAT is available from the SWAT web site, at
http://swat.tamu.edu/software/qswat/
Chris
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