Permafrost landscapes experience different disturbances and store large amounts of organic matter, which may become a source of greenhouse gases upon permafrost degradation. We analysed the influence of terrain and geomorphic disturbances (e.g. soil creep, active-layer detachment, gullying, thaw slumping, accumulation of fluvial deposits) on soil organic carbon (SOC) and total nitrogen (TN) storage using 11 permafrost cores from Herschel Island, western Canadian Arctic. Our results indicate a strong correlation between SOC storage and the topographic wetness index. Undisturbed sites stored the majority of SOC and TN in the upper 70 cm of soil. Sites characterised by mass wasting showed significant SOC depletion and soil compaction, whereas sites characterised by the accumulation of peat and fluvial deposits store SOC and TN along the whole core. We upscaled SOC and TN to estimate total stocks using the ecological units determined from vegetation composition, slope angle and the geomorphic disturbance regime. The ecological units were delineated with a supervised classification based on RapidEye multispectral satellite imagery and slope angle. Mean SOC and TN storage for the uppermost 1 m of soil on Herschel Island are 34.8 kg C m-2 and 3.4 kg N m-2, respectively. Copyright © 2015 John Wiley & Sons, Ltd.