Persistent organic pollutants (POPs) are hydrophobic substances that readily sorb to organic matter in particles and colloids instead of being freely dissolved in the water phase. This sorption affects the bio­availability and environmental transport of the POPs. The major part of this thesis concerns the role of sediments as secondary sources of POPs. As the primary emissions decrease, contaminated sediments where POPs have accumulated can become the main source of contamination. If the contaminated sediment by time becomes covered with cleaner layers, the POPs are buried and no longer in contact with the aquatic environment. Experiments in this thesis showed, however, that new invading species can alter the sediment-water dynamics as a result of their bioturbation, i.e. mixing of sediment particles and pore-water. Marenzelleria spp., invading species in the Baltic Sea that burrow deeper than native species, were found to increase the remobilization of buried contaminants. The sediment-to-water flux was inversely related to the burial depth (2-10 cm) of the POP congeners (polychlorinated biphenyls (PCBs) and polybrominated diphenyl ethers) and also inversely related to the hydrophobicity of the congener. The flux was therefore most pronounced for less hydrophobic contaminants, which was linked to the bioirrigating behaviour of these species. Marenzelleria spp. also accumulated the buried POPs and increased concentrations in surface sedi­ment. Contaminants previously considered buried at a ’safe’ depth can thus be remobilized as a result of the invasion of Marenzelleria spp. in the Baltic Sea. One method to decrease the remobilization of contaminants from sediments is ’capping’, i.e. a layer of clean material is placed as a cap on the sediment. By amending the cap with active materials, which sequester the POPs and decrease their availability, thinner layers can be used (’active capping’ or ’thin-layer capping’). Results from an experiment with thin-layer capping using different active materials (activated carbon (AC) and kraft lignin) showed that both the sediment-to-water flux and the bioaccumulation by benthic species of polychlorinated dibenzo-p-dioxins and dibenzofurans (PCDD/Fs), hexachlorobenzene (HCB) and octachlorostyrene (OCS) decreased with increased thick­ness of the cap layer (0.5-5 cm). Amendments with active materials further increased the cap efficiency. AC was more efficient than kraft lignin, and a 3 cm cap with 3.3% AC reduced the flux and bioaccumulation with ~90%. The reduction of the sediment-to-water flux was inversely related to the hydrophobicity of the POP, and reductions in the flux had similar magnitudes as reductions in the concentration in deep-burrowing polychaetes, demonstrating the importance of bioturbation for sediment-to-water transport. In a one-year study on the levels of PCDD/Fs, PCBs, and HCB in a coastal area of the Baltic Sea, the correlations between the POP levels and the levels of particles and organic carbon in the water were found to differ for POPs of different structure and hydrophobicity. The levels of PCDD/Fs decreased to one third in May, which could be related to the increased sedimentation, i.e. water-to-sediment transport, during spring bloom.