The McMurdo Dry Valleys (MDV) is a polar desert on the coast of East Antarctica where ephemeral wetlands become hydrologically active during warm and sunny summers when sub‐surface flows are generated from melting snowfields. To understand the structure and function of polar wetland ecosystems, we investigated the hydroecology of one such wetland, the Wormherder Creek wetland, during the warm and sunny summer of 2008 – 2009, when the wetland was hydrologically reactivated. Conservative tracer (LiCl) was injected for a 2‐hour period into a stream above the wetland to determine flow path orientations and hydrologic residence times. Tracer results indicated that surface water is rapidly exchanged with wetland groundwater and wetland residence times may exceed two austral summers. Major ion concentrations were uniform in samples from surface water and shallow groundwater throughout the wetland. Microbial mats in the wetland had high autotrophic index values (the ratios of chlorophyll a [Chl‐a]/ash‐free dry mass [AFDM]), ranging from 9‐38 μg Chl‐a/mg AFDM, indicative of actively photosynthesizing mat communities. The diatom communities in the mats were relatively uniform compared to those in mats from regularly flowing MDV streams, with four endemic and one widespread diatom taxa of the genus Luticola accounting for an average of 86% of the community. These results indicate that the hydrologic characteristics of the wetland contribute to uniform geochemical conditions. In turn, uniform geochemical conditions may explain the high autotrophic index values of the microbial mats and relatively low spatial variation of the diatom community.