Increasingly changing patterns of human sea and sea floor use originate in political, economic and societal developments often motivated by the process of transition towards a green economy. Offshore wind farming has turned into a major agent of change with a set of expected cumulative ecological impacts. Coastal and shelf seas become contested, but at the same time politically recognised areas, with emerging conflicts rooted in different perceptions, values and attitudes of coastal people. Associated with our limited understanding of environmental regimes and ecosystem impacts of cumulative shelf sea modifications are fragmented frameworks, in policy and economic sectors often opposing the balancing approach of Marine/Maritime Spatial Planning (MSP). Mid and long-term management plans are further hampered by limitations faced in predicting long-term and regional climate change impact and future socio-economic and cultural developments. Planning under these circumstances is “planning under uncertainty”. Based on a brief analysis of offshore wind farming in the context of MSP the paper illustrates the role of science by highlighting the important complementary functions of disciplinary process oriented research versus interdisciplinary and transdisciplinary approaches in assessing and modelling the expected cumulative effects of large scale offshore wind farming. In light of recent global discourse about future Earth system science, challenges and the emerging global science initiative “Future Earth” (supported by the UN, and major research and funding institutions) key research questions and the relevance of applying a co-design approach inviting all actors and researchers to the framing process are discussed. The ultimate goal is to foster ecosystem-based management. It is most evident that scientific information needs to be provided to inform one of the major and unprecedented transformations on continental shelves which is motivated by a socio-political decision to move towards global sustainability in response to climate change and economic development. Designing appropriate social environmental assessment, forecasting, observations and involving the institutional and legal dimensions are central in this context.