Combatting eutrophication is currently a major challenge for policy makers in the Baltic Sea region, and it is likely to remain so in the decades to come. Although total nutrient loads to the Baltic Sea have recently declined, the gap between current loadings and those required to ensure the desired status is still substantial (Reusch et al. 2018). This Special Issue is dedicated to research that helps inform how the eutrophication challenge might best be addressed by improving our understanding of technological constraints, societal drivers of change, land uses, environmental policies, and innovative governance with stakeholder involvement. These issues are important for the current generation and those to come and are issues we must address in order to succeed in reducing nutrient loads to the desired levels to gradually achieve the desired good environmental status of the Baltic Sea. Currently, we witness a new era of water policies across the entire Baltic Sea region. Our changing climate is impacting on precipitation and runoff, and is also the reason why new EU climate policies seek to tie carbon sinks more visibly to carbon sources. Both these aspects have repercussions for water policies. Thus, solving eutrophication challenges requires sharpening of existing policies and instruments, as well as creating new insights and governance approaches with broad stakeholder involvement in a changing environment. In order to design coherent water and climate policies, and target and implement those policies more efficiently, policy makers need to combine new insights regarding the inhabitants in the region, the catchments, and the Baltic Sea itself. Such insights can be expected from soil scientists, agronomists, hydrogeologists, marine ecologists, economists, and social and policy scientists. What is needed is on the one hand effectively targeted governance at appropriate spatial and temporal scales, adapted to differing interests and motivations of citizens living around the Baltic Sea, and on the other hand fine tuning and co-designing of policies at local, national, Baltic Sea regional and EU level. This Special Issue brings together recent research from four BONUS-funded projects—BONUS BALTICAPP, BONUS GO4BALTIC, BONUS MIRACLE and BONUS SOILS2SEA—that comprised part of the ‘Viable Ecosystem’ and ‘Sustainable Ecosystem Services’ BONUS research programmes. The projects addressed these common concerns through somewhat different, but inter-related, themes. Key messages emphasized and discussed in the research papers of this Special Issue are summarized under four interlinked themes: Scenarios for the future, Policies and ecosystem services in water governance, Novel approaches for managing nutrients, and Advanced modelling from field level to the entire Baltic Sea region.