Comprehensive spatial and temporal data on sediment quality in the Adriatic Sea are lacking. Therefore, prior to planned anthropogenic interventions in the local marine environment, such as deepening of the Rovinj harbour, the results of physicochemical and ecotoxicological analyses of five local coastal sediments were compared with regional averages and SQGs of neighbouring countries. Analyses of sediment grain size, content of metals and heavy metals, PAHs and PCBs were performed according to standard protocols. Sediment quality was classified according to French legislation (N1 and N2 level) and sediment guidelines. The phytotoxicity of the eluates was studied by flax seed germination tests. The logistic regression models Pmax and Pavg were used to estimate the probability of toxic effects. Except for the open sea (S5), all other sediments had concentrations slightly higher than the N1 for some metals (Cu, Ni, Hg, Cr) or ΣPAHs, while the Rovinj harbour (S1) reached the N2 value for mercury. The phytotoxicity assay with sediment eluates showed inhibition of germination, root length and root biomass production, with an average phytotoxicity index (PI) ranging from 6.06% to 42.00%. Significant correlations of Pavg and Pmax values with phytotoxicity and other specific parameters were found. In general, according to the applied SQGs, there are no potential ecological impacts on the marine environment at any of the investigated sites, with the exception of site S1.