The investigation of the microtopographic controls on thermal and hydrologic conditions of the soil and consequently the carbon dynamics from Arctic regions is of major importance. Ecosystem respiration (ER) between microsites of the same tundra type could differ more than ER in different tundra types even at different latitudes. In this study we investigated the microtopographic effect on soil temperature, thaw depth, pH, oxidation reduction potential (ORP), electrical conductivity (EC), dissolved CO2, vegetation types, and ER rates from different features forming the low-center polygon structure. Most of these environmental variables significantly differ particularly between areas with higher elevation (polygon rims) and with lower elevation (low-center polygons). Polygon rims presented the lowest water table and showed the lowest thaw depth and the highest ER (a seasonal average of 1 μmol CO2 m−2 s−1), almost double than the ER in the low-center polygons (a seasonal average of 0.6 μmol CO2 m−2 s−1). The microtopographic gradient from polygon rims to low-centers led to a very consistent pattern in pH, EC, ORP and dissolved CO2, with low-centers presenting the highest pH, the highest EC, the highest dissolved CO2, and the lowest ORP. Based on vegetation measurements, we also showed that microtopography controls the lateral flow of organic matter, and that vascular plant material accumulates as litter in the lower elevation areas, possibly contributing to the higher dissolved CO2 in the low-center polygons. Microtopography, and the ramifications discussed here, should be considered when evaluating landscape scale environmental controls on carbon dynamics in the Arctic.