Most of the primary production of the world's oceans takes place in the water column, thereby fuelling not only marine pelagic food-webs, but also most benthic communities. In addition, nearly all marine organisms depend on the pelagic zone for some part of their life-cycle. Although most contaminants have physico-chemical properties that cause them to associate with organic material particles and eventually be transported to sediments, direct contaminant inputs are predominantly to pelagic ecosystems. Taking both the ecological importance and the contaminant load into account, there is a surprising lack of scientific knowledge concerning the effects of contaminants in pelagic systems. The main reasons are presumably the difficulty in linking exposure with processes at a scale relevant for environmental management, and challenges involved in using pelagic fish and zooplankton species for experimental studies (excluding the 2-3 copepod species used for regulatory toxicity testing). Contaminants have been shown to affect primary producers as well as secondary producers-consumers, but there is very limited knowledge about ecological impacts. Top predators in marine ecosystems (piscivorous fish species, marine mammals, seabirds) will be particularly at risk from persistent organic contaminants since they will biomagnify. Although there is evidence of effects caused by such substances in the past, there is a need for continuous updates including “new” contaminants. Most relevant for lower trophic levels, micro- and mesocosm studies under controlled conditions are critical for increased understanding of processes and putative effects of contaminants in the pelagic zone. Some field-based strategies have been suggested and implemented to varying degrees for environmental management of contaminants in the water column, including riskbased modelling, bioassay-analyses of environmental samples or extracts (e.g., through the use of passive samplers), caging of organisms and, finally, collection and analyses of native organisms.