Supraglacial streams are important hydrologic features in glaciated environments as they are conduits for the transport of aeolian debris, meltwater, solutes and microbial communities. We characterized the basic geomorphology, hydrology and biogeochemistry of the Cotton Glacier supraglacial stream located in the McMurdo Dry Valleys of Antarctica. The distinctive geomorphology of the stream is driven by accumulated aeolian sediment from the Transantarctic Mountains, while solar radiation and summer temperatures govern melt in the system. The hydrologic functioning of the Cotton Glacier stream is largely controlled by the formation of ice dams that lead to vastly different annual flow regimes and extreme flushing events. Stream water is chemically dilute and lacks a detectable humic signature. However, the fluorescent signature of dissolved organic matter (DOM) in the stream does demonstrate an extremely transitory red-shifted signal found only in near-stream sediment leachates and during the initial flushing of the system at the onset of flow. This suggests that episodic physical flushing drives pulses of DOM with variable quality in this stream. This is the first description of a large Antarctic supraglacial stream and our results provide evidence that the hydrology and geomorphology of supraglacial streams drive resident microbial community composition and biogeochemical cycling.