There is an increasing demand for assessing ecosystem functions for freshwater wetlands, especially when comparing or prioritizing among wetlands at the watershed scale. We estimated the relative potential of selected ecosystem functions for freshwater wetlands within a watershed using widely available geospatial data. We developed four functions to estimate 1) flood storage, 2) late season flow, 3) sediment retention and 4) temperature control in four pilot watersheds in Oregon (Tualatin, Coquille, Upper Grande Ronde and Sprague). These watersheds are geographically separated from each other representing diverse ecoregion environments. Spatial analysis and geographic information system (GIS) were designed for maximum re-use, based on publicly-available data, commonly-used software, semi-automated techniques and wetland characterizations that attempt to capture fundamental wetland processes. Our data sources include 30-meter digital elevation models, NRCS soil survey extracts, USGS National Land Cover Data, USGS HUC8 boundaries (polygons) and statewide wetland delineations (polygons) processed within ArcGIS 10.2 and Python 2.7.5 software. Model parameters were compiled using multiple proxy values for size, slope, aspect, proximity, flow path distance, hydrologic gradient, shade, and soil characteristics. WPT characterizations emphasize the multi-faceted value of freshwater wetlands, relating potential within a watershed as well as providing model-based characterizations between watersheds. Our wetland prioritization tool (WPT) provides useful information to estimate and compare the relative potential for selected wetland functions, thereby improving success in wetland conservation, restoration, and mitigation efforts.