As activities such as fishing, mining, and bioprospecting head into the deep ocean, scientists work to produce knowledge that can inform sustainable and equitable management. The governance of deep-ocean activities therefore depends on how science renders the deep ocean knowable in policy and public arenas. Yet dominant analyses of deep ocean governance insufficiently account for how the everyday work of scientific knowledge production simultaneously anticipates, enacts, and legitimises particular ocean futures. This blind spot obscures the ways in which scientists and scientific institutions function as de facto governors of the deep ocean, not only by supplying evidence for policy debates, but also by shaping meaning through the performance of their scientific activities. Through a sociological analysis of data production onboard research vessels, this work shows how routinised and “invisible” selections and omissions can fundamentally shape scientific understandings of the deep ocean, which in turn inform and determine future governance decisions. As demands and impacts upon the deep ocean grow and knowledge needs becomes more complex, social science approaches can help deep ocean governance become more flexible and open to alternative approaches to knowing and interacting with the deep ocean.