Severe environmental problems documented in the Baltic Sea in the 1960s led to the 1974 creation of the Helsinki Convention for the Protection of the Marine Environment of the Baltic Sea Area. We introduce this special issue by briefly summarizing successes and failures of Baltic environmental management in the following 40 years. The loads of many polluting substances have been greatly reduced, but legacy pollution slows recovery. Top predator populations have recovered, and human exposure to potential toxins has been reduced. The cod stock has partially recovered. Nutrient loads are decreasing, but deep-water anoxia and cyanobacterial blooms remain extensive, and climate change threatens the advances made. Ecosystem-based management is the agreed principle, but in practice the various environmental problems are still handled separately, since we still lack both basic ecological knowledge and appropriate governance structures for managing them together, in a true ecosystem approach.