•A social-ecological viewpoint to analyze ecosystem services (ESS) is proposed.•Two types of ESS flow, direct and mediated, are defined.•A time lag can be identified in the generation of some ESS.•The viewpoint proposed can contribute to the management of social-ecological systems. The assessment of ecosystem services (ESS) requires approaches that are capable to deal with the complexity of social-ecological systems (SES). A new viewpoint is proposed, in which the social-ecological perspective of Ostrom’s SES framework is used to describe the flow of ESS, through the identification of the social and ecological elements involved. Two types of ESS flow emerge from this analysis, depending on the way in which the elements of ESS supply (resource system and resource units) and demand (actors) interact: (i) a “direct flow type” in which the resource units deliver the ESS through some specific ecological functions (e.g. wetlands providing carbon sequestration), and (ii) a “mediated flow type” in which the resource units become themselves the ESS when “used” by means of human activities (e.g. fish harvested through fishing activities). The identification of activities is crucial to understand the interactions between ESS, because of the feedbacks they produce on the ecosystem functioning and thus on the provision of the same or other ESS. In addition, these feedbacks can depend on temporal aspects of ESS provision. On these regards, a hypothesis is proposed according to which a time lag can exist between the ESS supply-side and flow in human-modified SES. Altogether, this social-ecological analysis of ESS can contribute to focus the management strategies on the control of impacting activities and on the maintenance of those processes which underpin ESS’ provision, thus contributing to the implementation of an ecosystem-based management of SES. These aspects are discussed in the light of the Venice lagoon example.