Aquatic ecosystems that have become degraded under stress show similarities both in the signs of pathology and in the mechanisms that promote degradation. A review of the transformations in several aquatic systems, including the Laurentian Great Lakes (Canada/US), the Baltic Sea (Finland) and Lake Chapala (Mexico) reveals signs of ‘ecosystem distress’, including alterations in primary and secondary productivity, nutrient cycling, species diversity and biotic composition. A shift from a predominantly vertical to horizontal nutrient spiraling characterizes all three aquatic ecosystems, as does a reduction in the abundance of the larger (high-valued) fish stocks. Once the health of robust systems begins to decline, mechanisms are called into play that tend to perpetuate the ecosystem breakdown. The process may be difficult to reverse, even when sources of initial stress are removed.