Ecosystem services (ES) are theoretically linked to healthy ecological conditions, but this relationship seems to be rather challenging to demonstrate in the real world. Therefore, shedding light on these aspects can be crucial for implementing effective ecosystem management strategies, for instance within the context of the EU Water Framework Directive (WFD) implementation. This work aims to present a spatially-explicit assessment of the ecological potential (capacity) and actual use (flow) of 12 ES in the Venice lagoon and to explore the relationships with the ecological status. Quantitative indicators of capacity and flow for each ES have been assessed and mapped and the results summarised with a set of aggregated indicators. The outcomes reveal a positive relationship between the overall capacity and flow of ES, suggesting that where the first is degraded, an overall loss of ES delivery occurs. A complex picture emerges when exploring the links with the ecological conditions, as the relationship changes with the ES and ecological status indicators considered. Structural indicators of ecological status, such as the Biological Quality Elements adopted by the WFD (assessed by MAQI and M-AMBI metrics), seem to be weakly linked with ES, while functional indicators (Kempton Q-90 diversity and secondary production) showed stronger links, especially when aggregated ES indicators are considered. Concerning different ES, it appears that the flow of the ES that are mediated by human uses (provisioning and cultural ES) is negatively related with some of the ecological status indicators. Finally, our results suggest possible limitations of the zonation adopted under the WFD, when it comes to the analysis of ES. We argue that ES could play a role in the management of the Lagoon ecosystem, as their analysis could be used to preserve the ecological functioning by managing the ‘uses’ we make of the ecosystem.