This article demonstrates a working method to automatically detect and prune portions of waterbody polygons to support creation of a multi‐scale hydrographic database. Water features are sensitive to scale change, therefore multiple representations are required to maintain visual and geographic logic at smaller scales. Partial pruning of polygonal features – such as long, sinuous reservoir arms, stream channels too narrow at the target scale, and islands that begin to coalesce – entails concurrent management of the length and width of polygonal features as well as integrating pruned polygons with other generalized point and linear hydrographic features to maintain stream network connectivity. The implementation follows data representation standards developed by the US Geological Survey (USGS) for the National Hydrography Dataset (NHD). Portions of polygonal rivers, streams, and canals are automatically characterized for width, length, and connectivity. This article describes an algorithm for automatic detection and subsequent processing, and shows results for a sample of NHD subbasins in different landscape conditions in the US.