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The levels and speciation of dissolved, particulate and gaseous Se have been measured in five thermokarst ponds in a sporadic and discontinuous permafrost region of northern Québec (Canada) during summer oxygen stratification. Evolution of Se concentrations with depth was investigated in sediment cores collected in three different ponds. The potential for inorganic Se transformation in natural pond waters was investigated by experimental incubations of isotopic species-specific tracers of selenite and selenate. Experimental and monitoring observation revealed that high dissolved carbon concentration, suspended particle matter concentration, heterotrophic activity and periphytic biofilms have a significant role in the formation of gaseous selenium species. In sediment, Se is mainly associated with organic matter in the concentration range 0.14–1.6 mg kg−1. Despite low outgassing rates of volatile Se toward the atmosphere (1–97 ng Se m−2 day−1), the large surface occupied by ponds in northern Canada may lead to important exchange rates (ca. 1 ton year−1) at the global scale. Detailed measurements of Se speciation, including volatile compounds, and its reactivity toward heterotrophic activity in selected thaw ponds from the Canadian Subarctic provides new insight to better constrain the biogeochemical pathways leading to Se removal from the water column via atmospheric gas exchange and sediment accumulation. [ABSTRACT FROM AUTHOR]