In the estuaries, sediments may represent both a sink and a secondary source of metals, due to the various biological and physico-chemical processes which control the metal dynamics in the sediment and the overlying water column. To evaluate the sediment contamination by metals and to identify the main metal input pathways, surface sediments were sampled at 40 locations in the Krka River estuary, an environment so far regarded as relatively unpolluted. To study the dynamics of metal behaviour in the estuarine environment and to quantify metal exchanges at the sediment water interface, sediment cores were retrieved from 7 locations within the estuary. To achieve research objectives, a comprehensive approach was used, which included geochemical characterization of dissolved (pore water) and solid fraction of the sediment and the overlying water column, determination of mineralogical and granulometric composition of the sediment, measurement of physico-chemical parameters of the sediment and water column and dating of one sediment core. Two distinct areas were distinguished; the upper unpolluted estuary and the lower estuary where sediment profiles reflected the history of anthropogenic metal input associated with the city of Šibenik. Three main point sources of contamination were identified: the former Electrode and Ferroalloy Factory, the Port of Šibenik and nautical marina/repair shipyard. The mobility of metals in the sediment was mainly controlled by the degradation of organic matter, either through primary redox reactions in the sediment, such as reductive dissolution of Fe and Mn oxyhydroxides by which metals are released to the pore water, either through secondary reactions which may remove metals from the pore water through formation of the authigenic phase or increase metals solubility by forming metal-DOM, metal-(poly)sulphide or metal-sulphide-DOM complexes. According to calculated benthic diffusive fluxes, sediment in the Krka River estuary is dominantly acting as a source of metals.