The geochemistry of pore waters from sediments deposited in the semi-enclosed bay of the Zrmanja River estuary, encompassing two small interconnected basins, the Novigrad Sea and the Karin Sea, was investigated. The conducted research aimed to identify diagenetic processes occurring in surficial bottom sediments and to assess the impact of these reactions on trace element concentrations in the overlying water. Sediment pore waters were extracted from sediment cores in a nitrogen atmosphere. Multielemental analysis of prepared samples was performed by high-resolution inductively coupled plasma mass spectrometry (HR-ICP-MS). All samples were analysed for the total concentration of 15 elements (As, Ba, Co, Cr, Fe, Li, Mn, Mo, Ni, Rb, Sb, Sr, Ti, U and V). Results indicate enrichment of sediment pore waters in the majority of measured elements relative to the estuary water. Degradation of organic matter and dissolution of Mn-Fe-oxyhydroxides under suboxic and anoxic conditions were identified as principal sources of dissolved cations in the studied pore waters. While sediments from the Novigrad Sea act as a permanent geochemical sink, the estimated fluxes for the Karin Sea sediments indicate transfer of certain elements from the sediment back to the water column, amounting to ~ 0.3 μg m−2 day−1 for Co, Ti and U; ~ 0.7 μg m−2 day−1 for As; between 1 and 5 μg m−2 day−1 for Mo, Ni and Ba; and ~ 70 μg m−2 day−1 for Fe and Mn. In the Zrmanja River estuary, the observed differences in the sediment pore water geochemistry and the role of the sediments in terms of mass exchange at the sediment-water interface could not be solely attributed to the sediment particle characteristics, but are considered to be a combined effect of organic matter input and local hydrogeological setting.