Climate change poses a substantial threat to the stability of the Arctic terrestrial carbon (C) pool as warmer air temperatures thaw permafrost and deepen the seasonally-thawed active layer of soils and sediments. Enhanced water flow through this layer may accelerate the transport of C and major cations and anions to streams and lakes. These act as important conduits and reactors for dissolved C within the terrestrial C cycle. It is important for studies to consider these processes in small headwater catchments, which have been identified as hotspots of rapid mineralisation of C sourced from ancient permafrost thaw. In order to better understand the role of inland waters in terrestrial C cycling we characterised the biogeochemistry of the freshwater systems in a c. 14 km2 study area in the western Canadian Arctic. Sampling took place during the snow-free seasons of 2013 and 2014 for major inorganic solutes, dissolved organic and inorganic C (DOC and DIC, respectively), carbon dioxide (CO2) and methane (CH4) concentrations from three water type groups: lakes, polygonal pools and streams. These groups displayed differing biogeochemical signatures, indicative of contrasting biogeochemical controls. However, none of the groups showed strong signals of enhanced permafrost thaw during the study seasons. The mean annual air temperature in the region has increased by more than 2.5 °C since 1970, and continued warming will likely affect the aquatic biogeochemistry. This study provides important baseline data for comparison with future studies in a warming Arctic.