Krossfjord-Kongsfjord system situated on the west coast of Svalbard archipelago is an ideal location to investigate the impacts of climate change on the environment. As a consequence of global warming, metal concentrations in the Arctic region are increasing due to permafrost melting and changes in biological processes. Therefore, the fjord sediments were studied for identification of provenance, mobility, bioavailability, and potential toxicity of metals in the fjord environment. Finer sediments and organic matter were found to be higher away from the glacier outlets, while coarser sediments were found to be higher near the glacier head. Illite, kaolinite, and chlorite constituted the clay mineral assemblage which had slightly influenced the metal distributions. The variations in metal abundance were attributed largely to the glacial activity along with the influence of Atlantic water mass in western Spitsbergen. Fjord system received sediment from the weathering of rocks indicating an input of terrigenous material. Comparison of metals in bulk sediment with Arctic sediment quality guidelines (ASQGs) showed that Zn and Cu were enriched in the sediment. However, to avoid the overestimation of the risk associated, fractionation of the metals was carried out which revealed higher Mn and Co in labile phases that pose a considerable risk to the biota.