Soil nutrient pools in the dry low Arctic are likely to be released under climatic change and this bioavailability has the potential to increase both terrestrial and aquatic productions. As well as the direct effect of warming, external disturbances such as nutrient deposition and grazing can also drive ecosystem change. This study in the low Arctic Kangerlussuaq area of southwest Greenland compared soil nutrient pools in terms of both topographic position on a catena and by soil depth in two small catchments with contrasting muskox abundance. We tested the hypotheses that there were differences between soil carbon (C), nitrogen (N) and phosphorus (P) across a soil catena (ridge ‐ slope ‐ valley) and by soil depth (litter ‐ 0–5 cm ‐ 25–30 cm) for the two sites (SS17b, muskox present, versus ‐ SS85, no muskox). Total C and N concentrations of soils were on average lower at SS17b compared to SS85. Moreover, the soil N concentration increased downslope in the catena with higher amounts in the valleys compared to the slopes and ridges. Soil P concentration (0.70 g P kg−1) was similar between catchments; however, litter P content was substantially different. The difference in soil nutrients between the two catchments was most likely due to the presence of muskox at SS17b, and hence grazing associated processes (defecation, altered microbiology and nutrient cycling). This study emphasises the heterogeneity of arctic landscapes and need for ecosystem specific research. Highlights: Soil nutrient pools in two low‐arctic catchments in Greenland were compared. Grazing and dung inputs by muskox affect soil nutrient pools in Greenland. Soil P stores in Kangerlussuaq are similar to intensively managed farmland in Europe. The heterogeneity of arctic landscapes and need for ecosystem‐specific research are emphasised.