This case study of Kongsfjorden, western coastal Svalbard, provides insights on how freshwater runoff from marine- and land-terminating glaciers influences the biogeochemical cycles and distribution patterns of carbon, nutrients, and trace elements in an Arctic fjord system. We collected samples from the water column at stations along the fjord axis and proglacial river catchments, and analyzed concentrations of dissolved trace elements, together with dissolved nutrients, as well as alkalinity and dissolved inorganic carbon. Statistical tools were applied to identify and quantify biogeochemical processes within the fjord that govern the constituent distributions. Our results suggest that the glacier type affects nutrient availability and, therefore, primary production. Glacial discharge from both marine-terminating glaciers and riverine discharge from land-terminating glaciers are important sources of dissolved trace elements (dAl, dMn, dCo, dNi, dCu, and dPb) that are involved in biological and scavenging processes within marine systems. We identified benthic fluxes across the sediment-water interface to supply fjord waters with silicate, dFe, dCu, and dZn. Our data show that intensive carbonate weathering in proglacial catchments supplies fjord waters with additional dissolved carbonates and, therefore, attenuates reduced buffering capacities caused by glacial runoff. Our study provides valuable insight into biogeochemical processes and carbon cycling within a climate-sensitive, high-latitude fjord region, which may help predict Arctic ecosystem changes in the future.