We identified an objective set of 25 commonly available ecosystem metrics applicable across the world's large continental freshwater and brackish aquatic ecosystem. These metrics measure trophic structure, exploited species, habitat alteration, and catchment changes. We used long-term trends in these metrics as indicators of perturbations that represent an ecosystem not in homeostasis. We defined a healthy ecosystem as being in a homeostatic state; therefore, ecosystems with many changing trends were defined as more disturbed than ecosystems with fewer changing trends. Healthy ecosystems (lakes Baikal, Superior, and Tanganyika) were large, deep lakes in relatively unpopulated areas with no signs of eutrophication and no changes to their trophic structure. Disturbed ecosystems (lakes Michigan, Ontario, and Victoria) had shallow to moderately deep basins with high watershed population pressure and intense agricultural and residential land use. Transitioning systems had widely varying trends and faced increasing anthropogenic pressures. Standardized methodologies for capturing data could improve our understanding of the current state of these ecosystems and allow for comparisons of the response of large aquatic ecosystems to local and global stressors thereby providing more reliable insights into future changes in ecosystem health.