The Venice lagoon social-ecological system is characterized by a strong relationship between the natural environment and human activities. This is especially noticeable in the aquaculture and hunting reserves of the lagoon, locally known as valli da pesca. Previous works about Ecosystem Services (ESs) in the Venice lagoon focused on the so-called “open lagoon”, overlooking the role of the valli da pesca. Nonetheless, despite being completely managed ecosystems, the valli da pesca have conserved typical elements of transitional water environments that the other parts of the lagoon have lost. By evaluating nine ESs using a spatially explicit approach, we found that the valli da pesca, despite covering 17% of the surface, are contributing for 38% of the ESs total capacity, and for 24% of the ESs total flow, in comparison to the open part of the lagoon. Moreover, the management that aims to maximize in a perspective of sustainability some provisioning ESs, such as extensive aquaculture, can positively influence the presence of factors on which other ESs capacity is also based. As a result, the open lagoon benefits from a sort of spill-over effect for lifecycle support, hunting, and cultural ESs such as tourism, information for cognitive development, and birdwatching. Such significant contributions could be endangered in the context of a lagoon subjected to increasing pressures from anthropic activities, where adaptations to impacts, as well as to climate change and sea-level rise effects, in the long run, will modify the lagoon hydrodynamics and the sea-lagoon connectivity, threatening the valli da pesca and so their ESs supply.