A Svalbard Science Forum workshop about research on the Kongsfjorden System was held in Ny-Ålesund, 28-31 March 2008. The aim was to discuss focal areas for future research and to initiate the Kongsfjorden System Integrated Research Flagship. Current work and future plans of the individual research groups in Ny-Ålesund related to the Kongsfjorden System were presented. This built the base for identifying knowledge gaps and following future research priorities were identified: There is a great need to combine the atmospheric measurements of long-range pollutants with measurements of the contaminant levels in the biota, to study the feedback mechanisms from the biosphere to the atmosphere and to investigate the interactive effects of rising temperatures and enhanced UV- radiation. Furthermore, knowledge is little about the changes in the pelagic fish community of Kongsfjorden, a monitoring programme for phytoplankton is needed and data on organic carbon mineralization is lacking. Also, the knowledge about water exchange processes in the fjord and small scale turbulences should be improved. Finally, it was suggested to use clams as environmental indicators. Two major infrastructure innovations were suggested, a cabled oceanographic monitoring platform that will allow real-time data retrieval and an integrated comprehensive monitoring station on the central islands within Kongsfjorden to monitor and study the processes on the atmosphere/ocean surface interface. It was also emphasised that a database for long-term data series from the Kongsfjorden System needs to be established and made available for the research community, as well as the metadatabases already established have to be coordinated and further developed. Several initiatives were proposed that will contribute to an integrated approach to better understand the seasonal and annual dynamics of the Kongsfjorden ecosystem in the light of pollutant effects and climate change: The monitoring programme of atmospheric pollution at the Zeppelin Station will be further developed and linked to the marine research activities in order to identify the major drivers influencing the atmosphere/ocean surface interface. This will be supplemented by a marine monitoring platform that will allow real time monitoring of oceanographic and biological parameters in the fjord. The effects of discharges of terrigenous organic carbon and terrestrial particles from permafrost soils on the physiology of benthic organisms will be investigated. It is suggested that Kongsfjorden should be established as a main reference system for studies on the transport patterns of anthropogenic and natural contaminants throughout the marine foodweb and the consequences for the biota communities. Also, the variability of abiotic conditions and the effects on the biota will be addressed. The alteration of algae spring bloom needs to be studied in the light of observed changing oceanographic parameters and the possible consequences for the higher trophic levels. Furthermore, clams will be used as indicators for changes in climate and environmental parameters due to their behavioural modulations as response to environmental parameters. A special emphasis will be to advance the understanding of overwintering strategies of key components of the Kongsfjorden ecosystem.Also, climate data on longer time-scales than the instrumental records are needed to assess the significance of the current warming in the context of the Holocene and to produce more reliable predictions for the future climate.