The main aim of the present study was to compare the quality of particle emissions (urban runoff and settling particles in rivers and harbours) to the quality of top-layer bed sediments, for two Norwegian harbours (Oslo and Drammen). A sub-aim was to investigate whether non-industrial urban runoff contributed to the organotin load of sediments, apart from leaching from ship hulls. Time-integrated samples of stormwater runoff were obtained in an innovative manner, by sampling man-holes in the stormwater system. Settling particles were sampled with sediment traps. The study focused on PAHs, PCBs and organotin compounds. Contaminant levels were generally a factor of 2-10 (PAHs) and 3-30 (TBT) lower in emitted riverine and runoff particles than in top-layer bed sediments, except for PCBs in Oslo harbour (only 20-30% lower). Significant levels of tributyltin (TBT; median 140mug/kg) were shown in runoff particles, showing that TBT can also be emitted via urban sources, since the sampled man-holes were not in areas where dry-docking activities take place. Possible land-based TBT sources include long-lasting house paint and use of TBT as PVC stabilizer and timber preservative. Since there are ongoing emissions into the two studied harbour areas, it is concluded that the addition of an actively sorbing capping material such as activated carbon might be the best remediation alternative.