This work introduces methodological novelties in the field of trace metal speciation and organic matter in natural waters: (i) advancement of competitive ligand exchange - adsorptive cathodic stripping voltammetry; a new modes of multi detection window approach, (ii) revised application of copper (Cu) ion-selective electrodes in high chloride media i.e., seawater and (iii) a novel voltammetric method for quantification of humic substances. The second chapter of the thesis is dedicated to field studies in the Krka River estuary: (i) the dynamics and seasonality of dissolved organic matter (DOM) in the estuary and (ii) organic Cu speciation in the estuarine salinity gradient, (iii) the dynamics of various trace elements (Cu, Zn, Pb, Cd, Ni, Co, Cr, Fe, Mn, Al, As, V, U) and DOM in the estuarine surface microlayer (SML) and (iv) the size partitioning of different trace metals (Cu, Zn, Pb, Cd, Ni, Co, Fe, Mn and Al) in the salinity gradient. In winter, the estuarine waters contained a strong terrestrial signature, whereas in summer in situ production dominated the DOM pool. The high stratification combined with a decoupling between production and removal processes resulted in DOM accumulation above the halocline. In the bottom layer, DOM was released and quickly removed when oxygen was available, whereas in hypoxic waters the production of dissolved organic carbon and chromophoric DOM was linearly related to oxygen consumption. The Cu speciation study identified two ligand classes: L1 (12.5 < logK’CuL1 < 14.3) was mainly derived from recent phytoplankton production and L2 (10.6 < logK’CuL2 < 11.1) was characterised as predominantly humic substances of both terrestrial and autochthonous origin. Seasonal anthropogenic Cu input was successfully buffered by the ambient ligand pool due to the increased ligand concentrations in summer attributable to increased in situ production. The extensive SML samplings gave insights in diel variations of total and dissolved concentrations of trace elements in the SML, which were influenced by various factors: wind speed and wind direction, suspended particulate matter (primarily Fe, Al, Mn and Pb), complexation with organic ligands and bubble scavenging (primarily Fe, Cu and Pb) and bacterioneuston activity. The truly dissolved fraction (< 3 kDa) dominated the size speciation of Ni, Cd, Zn, Co and Cu, while Fe, Al, Pb and Mn were mainly present in particles larger than 5 μm. Of the studied metals, Pb, Al, Fe and Cu showed the highest affinity for colloids (3 kDa – 0.1 μm), which accounted for 30 – 37% of their dissolved pool (< 0.1 μm).