In the future, the world is expected to rely increasingly on renewable biomass resources for food, fodder, fibre and fuel. The sustainability of this transition to bioeconomy for our water systems depends to a large extent on how we manage our land resources. Changes in land use together with climate change will affect water quantity and quality, which again will have implications for the ecosystem services provided by water resources. These are the main topics of this Ambio special issue on “Environmental effects of a green bio-economy”. This paper offers a summary of the eleven papers included in this issue and, at the same time, outlines an approach to quantify and mitigate the impacts of bioeconomy on water resources and their ecosystem services, with indications of useful tools and knowledge needs.