The Kongsfjorden System in Svalbard is an established reference site for Arctic marine studies that hosts numerous, international, multidisciplinary collaborative science projects. Kongsfjorden (79 oN) represents an ideal natural laboratory in the Arctic and functions as a local indicator for climate change. Because of its open connection to Fram Strait, it is directly influenced by variable climate signals in the West Spitsbergen Current (Hop et al. 2006; Walczowski et al. 2012; Wassmann et al. 2015). Advection of Transformed Atlantic water into the fjord is important for its seasonal hydrography as well as its biological communities (Cottier et al. 2005, 2007; Hop et al. 2006; Willis et al. 2006, 2008; Dalpadado et al. this issue). In the past, the fjord was regularly covered by sea-ice (Gerland and Renner 2007), but because of increased advection of Atlantic water, regular winter ice cover has been rare since 2005/2006 (Cottier et al. 2007). The inner part of the fjord is still rather “Arctic” because it is influenced strongly by glacial run-off from large tidal glaciers (Karner et al. 2013; Schellenberger et al. 2015). Because of the dual Atlantic/Arctic inputs, the fjord houses pelagic and benthic communities that comprise a mixture of boreal and Arctic flora and fauna, which varies seasonally as well as interannually (Hop et al. 2002, 2012; Walkusz et al. 2009; Voronkov et al. 2013). Kongsfjorden and the adjacent atmospheric Zeppelin Station represent one of the most important environmental monitoring locations in the Arctic. Scientific data from Kongsfjorden have been sampled for more than 100 years, but it was not until the year 2000 that the first Kongsfjorden Ecosystem Workshop was held at the University Centre in Svalbard; 40 participants attended from France, Germany, Italy, Norway, Poland, Russia, Spain, Sweden and the UK. The results of this workshop were published in two well-recognized reviews focused on the physical environment of Kongsfjorden-Krossfjorden (Svendsen et al. 2002) and the ecosystem of Kongsfjorden (Hop et al. 2002). Research performed in Kongsfjorden at the Koldewey Station (AWI) during 1991-2003 was presented in a scientific report entitled The coastal ecosystem of Kongsfjorden, Svalbard (Wiencke et al. 2004). Research in Kongsfjorden was further discussed and coordinated during an international workshop in Ny-Ålesund in March 2008, which resulted in a document The Kongsfjorden System - a flagship programme for Ny-Ålesund (Gabrielsen et al. 2009). This flagship programme is currently followed up in Ny-Ålesund seminars, with bi-annual meetings to exchange scientific results, advancements, ideas and experience and to increase coordination and collaboration among researchers in Ny-Ålesund. Within the last decade, much new and important data have been obtained from the growing research community in Ny-Ålesund, now comprising 18 research stations from 11 nations. The new data were summarized and presented in a compact manner during a second Kongsfjorden Ecosystem Workshop held on 10-17 March 2014 at the conference facility Hamn i Senja, Skaland, Norway. This special issue is published in two parts and contains 34 original papers with new results mostly presented during the workshop, with some additional contributions. The papers cover most organism groups and processes relevant to the marine ecosystem from pelagic microbial heterotrophs over zooplankton to benthic micro- and macroalgae, macrozoobenthos, fishes and seabirds. An important section deals with sedimentation and pollutants in sediments. Effects of climate change on biological communities are addressed in several papers. Pertinent comparisons between Kongsfjorden and other fjord systems in Svalbard characterised by different environmental conditions give new insights into expected future changes in Kongsfjorden. Another focus is seasonality of marine organisms and communities, which also includes the winter season. Many studies include new information on biodiversity and trophic interactions.