The health of soil-sediment-water ecosystems is under pressure from economic activities and a changing climate. This decreases health and hampers the service provision capacity of these ecosystems and thus impacts human well-being. Protecting and where feasible restoring of ecosystem health has currently become the key European environmental policy objective and for this it is needed to take an entire system approach and engage stakeholders. ‘Entire’ means that soil, sediment and water are regarded as closely interlinked environmental matrices that need to be managed by taking a ‘river (or mountain) to sea’ perspective, crossing spatial, discipline, political and cultural boundaries. This paper presents a conceptual model to support that purpose. Essentially, the conceptual model presents an approach for ecosystem-based management aimed to achieve healthy ecosystems, i.e. soil-sediment-water ecosystems that have the continued capacity to support ecosystem services to the benefit of their users. The model proposes a cyclic (iterative, learning-by-doing) approach and integrates soil-sediment-water, ecosystems, ecosystem services, users (stakeholders), pressures, information, management strategy and program of measures as building blocks. To successfully apply the model, it is above all needed to take an entrepreneurial approach, i.e. leave comfort zones, take an adventurous road, learn together to manage together, be adaptive and consider other than only command-and-control solutions. Furthermore, authorities should become facilitative leaders to engage users in co-creation of an ecosystem-based management strategy. Real live and place-based experimenting with multiple stakeholders, such as in the Living Labs and Lighthouses that are proposed in the EU soil mission, may provide an ideal instrument for such application, i.e. where the conceptual model can be used and support the achievement of European environmental policy objectives.