Climate change is significantly modifying ecosystem functioning on a global scale, but little is known about the response of deep-sea ecosystems to such change. In the past decade, extensive climate change has modified the physico-chemical characteristics of deep waters in the eastern Mediterranean. Climate change has caused an immediate accumulation of organic matter on the deep-sea floor, altered the carbon and nitrogen cycles and has had negative effects on deep-sea bacteria and benthic fauna. Evidence from a miniature ocean model provides new ways of interpreting signals from the deep sea and indicates that, contrary to what might have been expected, deep-sea ecosystems do respond quickly to climate change.