Watershed pairing is an approach used to assess effects of restoration on a landscape by comparing conditions across a treatment watershed and a control watershed, and then quantifying the differences. When the watersheds are statistically paired, the control watershed can serve as a baseline of conditions compared to the treatment watershed. We apply a watershed pairing analysis across a series of five watersheds within a research ranch in Baja California Sur, Mexico. We use a Digital Elevation Model (DEM) to develop the watershed boundaries. We then collected a series of structural and biophysical traits to characterize the watersheds. Finally, we applied a hierarchical clustering analysis to identify the paired watersheds. This data release consists of a shapefile of the five watersheds with attributes for each of the structural and biophysical traits, in addition to an attribute identifying the direct pairs.