The coastal and archipelago waters of the northern Baltic Sea are influenced by increasing eutrophication (significantly increasing temporal trends in nutrient availability). Increased nutrient levels and pelagic primary production have led to decreased transparency in the water body, increased plankton biomass, and increased amounts of filamentous algae. Large-scale and long-term (15-30 years) comparisons have shown that zoobenthic communities have changed significantly (altered species diversity, increased total abundance and increased biomass). The stress in the ecosystem is also illustrated at the population level (Macoma balthica). An increasing trend is shown for a near-shore fish community, where the increase in biomass has been linear over the past twenty years. Significant predictability of the regression has been shown for 1989-1994. Some areas show signs of community recovery, or changes attributable to natural variation, whereas other nearby areas may display opposite trends. The paper illustrates: (a) overall long-term changes (abiotic: nutrients and turbidity; and biotic: primary production, zoobenthos and fish); (b) site- specific long-term dynamics (infaunal and fish communities); and (c) cases of alternating long-term recovery and deterioration (water quality, zoobenthos).