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Evaluation of the water storage in several ponds near Creswell Bay, Somerset Island, Canada, an area experiencing a polar desert climate (cool, moist), served to reveal factors that are important in the sustainability of these freshwater ecosystems within a larger wetland complex. Our study focused on the hydrology of 12 ponds of different sizes in various geomorphologic settings: moraine, bedrock, and coastal areas. A positive water balance plays an important role in the survival of the ponds experiencing variable climatic conditions and survival over the season depends largely on the local enrichment of water through various hydrologic linkages. Pond inputs and losses are governed by the pond catchment topography, substrate, hydrology, and seasonal climatic conditions. Low hydrologic energy and long hydroperiod (e.g., ponds in surface-flow dominated systems with multiple hydrologic linkages) are associated with a high degree of pond sustainability. Ponds with high hydrologic energy and short hydroperiods (e.g., ponds in precipitation and groundwater-dominated systems) show limited hydrologic sustainability. We suggest that these latter ponds in this polar desert environment will be the most vulnerable to future climate warming in the Canadian High Arctic.