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The North American Prairie Pothole Region covers about 770,000 square kilometers of the United States and Canada (including parts of 5 States and 3 provinces: North Dakota, South Dakota, Montana, Minnesota, Iowa, Saskatchewan, Manitoba, and Alberta). The Laurentide Ice Sheet shaped the landscape of the region about 12,000 to 14,000 years ago. The retreat of the ice sheet left behind low-permeability glacial till and a landscape dotted with millions of depressions known today as prairie potholes. The wetlands that subsequently formed in these depressions, prairie-pothole wetlands, provide critical migratory-bird habitat and support dynamic aquatic communities. Extensive grasslands and productive agricultural systems surround these wetland ecosystems. In prairie-pothole wetlands, the compositions of plant, invertebrate, and vertebrate communities are highly dependent on hydrogeochemical conditions. Regional climate shifts between wet and dry periods affect the length of time that wetlands contain ponded surface water and the chemistry of that ponded water. Land-use change can exacerbate or reduce the effects of climate on wetland hydrology and water chemistry. A mechanistic understanding of the relation among climate, land use, hydrology, chemistry, and biota in prairie-pothole wetlands is needed to better understand the complex, and often interacting, effects of climate and land use on prairie-pothole wetland systems and to facilitate climate and land-use change adaptation efforts. The Pothole Hydrology-Linked Systems Simulator (PHyLiSS) model was developed to address this need. The model simulates water-surface elevation dynamics in prairie-pothole wetlands and quantifies changes in salinity. The PHyLiSS model is unique among other wetland models because it accommodates differing sizes and morphometries of wetland basins, is not dependent on a priori designations of wetland class, and allows for functional changes associated with dynamic shifts in ecohydrological states. The PHyLiSS model also has the capability to simulate wetland salinity, and potential future iterations will also simulate the effects of changing hydrology and geochemical conditions on biota. This report documents the development of the hydrological and geochemical components of the PHyLiSS model and provides example applications.