With the fall of the Venetian Republic in 1797 and the subsequent transformation of nearly all sixty lagoon islands into military outposts, not only was an invaluable architectural heritage dismantled, but the very concept of a unified, interconnected archipelago was lost. During the early modern period, these water-bound settlements were crucial to Venice’s urban framework, encompassing a network of capillary infrastructures for the city’s supply, defence, healthcare as well as civic rituals. Today, however, these islands lie abandoned to the lagoon’s capricious waters, with their buildings, architectural elements, and spaces vanished along with their stories. Reconstructing this dilapidated cultural heritage therefore demands a dual focus on both the tangible architectural remnants and the intangible urban, economic, and socio-cultural threads that once wove the capital into its aquascape. The Venice’s Nissology project digitally recreates these peculiar environments in a 3D, interactive, and geospatial infrastructure that visualises, through time and space, the once-thriving islands in both their physical forms and social arrangements. This platform allows for the navigation of 3D interoperable models, seamlessly integrated with historical data and sources, which represent the spaces where to resemantise the long-lasting dynamics of Venice’s centre-periphery relations, re-evaluating the archipelago’s role as a fundamental connective tissue in the city’s urban practices.