The distribution, speciation, behaviour, and fate of selected trace metals (TM) (Zn Cd, Pb, Cu, Ni, and Co) were studied in the water column of the highly stratified Krka River estuary, from 2009 to 2013, covering two contrasting seasons (summer/winter). In addition, the study involved measurements of dissolved/particulate organic carbon (DOC/POC) and major physicochemical parameters (salinity, pH, dissolved oxygen, temperature). Water samples were taken from the three characteristic layers (brackish, the freshwaterseawater interface (FSI), and seawater). Stripping voltammetry (anodic, and adsorptive cathodic) was the primary analytical technique, while the diffusion gradient in thin films (DGT) technique was used as a complementary technique for speciation measurements. The concentrations of all TM were lower in the Krka River than in the open Adriatic which allowed the identification of pathways and processes governing the horizontal and vertical redistribution of TM across the whole estuary, whether they were added into the system by human activity or by in-situ processes (e.g. scavenging). Non-conservative behaviour for most of the studied TM observed in the surface layer of the estuary was primarily caused by their input in the Šibenik Bay area. Detailed "mapping" of the bay showed that the harbour and nautical marina are the regions with the highest concentrations of TM. A significant increase of Cu and Zn in the entire estuary transect during the summer period appeared to be directly linked to intensive nautical activity i.e. caused by the release of TM from antifouling paints. The scavenging of metals into the deeper layers, along with the longer residence time of seawater, caused an upstream increase in TM concentrations in the seawater layer. A very good agreement between the vertical profiles of DGT-labile, and dissolved TM concentrations suggests that the DGT technique can be successfully used to determine potentially bioavailable TM concentrations in estuarine conditions. The fraction of DGT-labile TM, which reflects their chemical speciation (primarily, their binding to natural organic ligands), ranged from > 90% for Cd, to < 20% for Cu, but also depends on the concentration ratios of metals and organic ligands. Voltammetric speciation of Cu showed the presence of two types of organic ligands that form strong (L1, 9.6 < logK1 < 11.9) and weak (L2, 7.8 < logK2 < 9.9) Cu complexes. The concentration of weak organic ligands (L2) is correlated with the DOC concentration, and is higher in summer, most probably due to the increased biological activity. The concentration of free Cu ions (the most bioavailable form), at ambient conditions, is regulated primarily by the complexation with strong ligands (L1). For most of the samples, the calculated free Cu slightly exceeds the toxic threshold of 10 pM. However, these values are the result of applied methodology of calculation, and does not necessarily reflect real ambient conditions