Human activities are shaping the Earth system and creating novel properties in the intertwined Social-Ecological Systems (SES). Although novelty is acknowledged in SES theories, the concept of novelty is not well understood, and little mathematical formalization and empirical foundations have been made. Building on the theoretical frameworks of Complex Adaptive Systems (CAS) and concepts of novelty in ecology, this licentiate thesis suggests a first attempt to quantify novelty in a marine ecosystem, in a SES context. Here, I focus on the past emergence of novelty in a marine SES to better understand when and where novelty has emerged and which drivers affect this emergence. Novelty emerges in a CAS when it has moved beyond its historical range of variation. The historical state depends on the temporal and spatial scale as well as the context of the study. Building on the characteristics of CAS, novelty is multidimensional, emerges on a continuum, can be nonlinear, and follows baseline specific trajectories. It has been quantified as the degree of dissimilarity of a system relative to a specific baseline. I used the case of the Baltic Sea SES, where long-term data exists, and many ecological, political, and economic changes have been recorded. Here, I focus on structural changes of the system rather than interactions and feedbacks. Paper 1 focuses on the ecological novelty in the Baltic Sea and contributes as the first study that quantifies novelty in marine ecosystems and across different trophic levels. Results reveal that over the 35-year study-period (1980-2015), novelty has emerged following the pattern of change, but at a slower pace. It has emerged in complex temporal and spatial pattern of the tested abiotic and biotic components. Both abiotic and biotic novelty showed a higher rate of novelty in confined northern basins than in the Central Baltic Sea, which indicated that some areas are more susceptible to the rise of novelty than others. Temperature and salinity were identified as the main abiotic drivers of biotic novelty in the Baltic Sea. Paper 2 contributes as the first study to quantify socio-economic novelty in a marine SES. Socio-economic novelty in the Baltic Sea showed a change in the contribution to novelty from factors linked to local and regional management levels, i.e., fishing gears and commercial groups, to trades which are linked to international level. A high increase in imports and exports in recent years marked the fastest increase in novelty over the period studied. In the latter, novelty in terms of economic value of fishery products was higher than their novelty in quantity. Sweden, Denmark, and Poland have been the countries contributing most to the emergence of novelty in the studied period. This paper illustrates that understanding socio-economic novelty together with ecological novelty, may provide a better understanding of the complexity of marine SES. Although not all the characteristics of CAS could be captured by the methodological approach used in Paper 1 and 2, many have been identified and considered. However, this highlights the need for more methods that can capture different characteristics of CAS, such as interactions and feedbacks, and more knowledge on the emergence of novelty in SES. Understanding how novelty emerges, its processes in different SES components and across-scales, may reduce the risk of missing opportunities for biodiversity conservation, and of unintended management outcomes for long-term sustainability.