Human activities are altering the processes that connect organisms within and among habitats and populations in marine and freshwater (aquatic) ecosystems. Connectivity can be quantified using graph theory, where habitats or populations are represented by ‘nodes’ and dispersal is represented by ‘links’. This approach spans discipline and systemic divides, facilitating identification of generalities in human impacts. We conducted a review of studies that have used graph theory to quantify spatial functional connectivity in aquatic ecosystems. The search identified 42 studies published in 2000–14. We assessed whether each study quantified the impacts of (1) habitat alteration (loss, alteration to links, and gain), (2) human movements causing species introductions, (3) overharvesting and (4) climate change (warming temperatures, altered circulation or hydrology, sea-level rise) and ocean acidification. In freshwater systems habitat alteration was the most commonly studied stressor, whereas in marine systems overharvesting, in terms of larval dispersal among protected areas, was most commonly addressed. Few studies have directly assessed effects of climate change, suggesting an important area of future research. Graph representations of connectivity revealed similarities across different impacts and systems, suggesting common strategies for conservation management. We suggest future research directions for studies of aquatic connectivity to inform conservation management of aquatic ecosystems.