The structure and function of the Mediterranean Sea Ecosystems (MSE) are rapidly changing. Global warming is the main driver of change, and the MSE responses are dramatic. The establishment of non-indigenous species, heavily influenced ecosystem functioning; human pressures such as overfishing, triggered regime shifts such as that from fish to jellyfish; the Eastern Mediterranean Transient changed the circulation patterns of the Eastern Mediterranean basin. Models did not predict these changes. Science, so far, focused much on the constraints that lead to regular sequences of events, allowing for predictions. In periods of rapid change, though, the historical nature of ecology becomes prominent, and contingencies acquire an overwhelming importance. This calls for new approaches to the study of complex systems, for instance with a shift from monitoring to observation, with a revival of natural history. The identification of cells of ecosystem functioning, based on oceanographic processes that enhance production at different levels of marine food webs in specific areas, is a challenge for future studies that will eventually lead to better management and protection of the marine natural heritage. Even if historical systems do not allow for predictions, some trends are clear and a set of possible scenarios of what will happen in the future Mediterranean Sea can be proposed.