Lagoons deliver invaluable ecosystem services because they represent an efficient filter for nutrients due to vital biogeochemical processes that are carried out by pelagic and benthic microorganisms as water flows through on its way to the sea. As being a barrier between land and sea, lagoons play an important yet poorly constrained role for Baltic biogeochemical cycles. Thus, the main aim of CycloN is to screen the complete nitrogen (N) cycle at gene and transcript level, and quantify a fate of N in the three largest European and Baltic lagoons (Curonian, Oder/Szczecin and Vistula Lagoons) across a seasonal nitrogen gradient. In the project, a complete N cycle in lagoon ecosystems will be characterized, and all processes measurements will be complemented by quantitative analysis of active RNA transcripts and genes, providing valuable new insights into the abundance, diversity, metabolism and biogeochemical activity of N-cycling microbial communities. These lagoons will stand as models to examine whether and how the seasonal shift from N excess to N limitation affects the activity of the microbial community, which in turn regulates N attenuation. Our results will be essential to achieve a good environmental status, which is required under the EU Marine Strategy Framework Directive and Baltic Sea Action Plan, to improve biodiversity and in general to meet the United Nations 14th sustainable development goal “Life Below Water”. Furthermore, the combination of traditional biogeochemistry (process measurements) with more recent functional genomics methods will allow 1) metatranscriptomic reconstruction of active N-cycling pathways, 2) based on DNA/RNA sequences to screen de novo assemblies for such type of ecosystems, 3) to provide new metabolic pathways, which can be potentially used in biotechnology.