The Venice lagoon—the largest Mediterranean coastal lagoon—is characterized by the presence at its edges of 31 “valli da pesca”, types of artificial ecosystems that mime the ecological processes of a transitional aquatic ecosystem. Constituted by a series of regulated lakes bounded by artificial embankments, the valli da pesca were established centuries ago to maximize provisioning Ecosystem Services (ESs), such as fishing and hunting. As time passed, the valli da pesca underwent an intentional isolation process leading to private management. Nonetheless, the valli da pesca are still exchanging energy and matter with the “open’ lagoon and today represent an essential element within the context of lagoon conservation. This study aimed to analyze the possible effects of artificial management on both ESs supply and landscape arrangements by assessing 9 ESs (climate regulation, water purification, lifecycle support, aquaculture, waterfowl hunting, wild food, tourism, information for cognitive development, and birdwatching), along with eight landscape indicators. Obtained results suggested that the valli da pesca are today ruled under five different management strategies, according to the maximized ES. Management conditions influence the landscape pattern and achieve a series of “side effects” on the other ESs. The comparison between the managed and abandoned valli da pesca highlights the importance of anthropogenic interventions for conserving these ecosystems, as the abandoned valli da pesca show a loss of ecological gradients, landscape heterogeneity, and provisioning ESs. Nevertheless, the persistence of intrinsic geographical and morphological characteristics still prevails regardless of intentional landscape molding. The result is that the provisioning ESs capacity per unit area is higher in the abandoned valli da pesca than in the open lagoon, emphasizing the importance of these confined areas of the lagoon ecosystem. Considering the spatial distribution of multiple ESs, the provisioning ESs flow that does not occur in the abandoned valli da pesca seems to be replaced by the flow of cultural ESs. Thus, the ESs spatial pattern highlights a balancing effect between different ESs categories. The results are discussed considering the trade-offs generated by private land conservation, anthropogenic interventions, and their relevance for the ecosystem-based management of Venice lagoon.