||Background Ecological attributes estimated from food web models have the potential to be indicators of good environmental status given their capabilities to describe redundancy, food web changes, and sensitivity to fishing. They can be used as a baseline to show how they might be modified in the future with human impacts such as climate change, acidification, eutrophication, or overfishing. Methodology In this study ecological network analysis indicators of 105 marine food web models were tested for variation with traits such as ecosystem type, latitude, ocean basin, depth, size, time period, and exploitation state, whilst also considering structural properties of the models such as number of linkages, number of living functional groups or total number of functional groups as covariate factors. Principal findings Eight indicators were robust to model construction: relative ascendency; relative overhead; redundancy; total systems throughput (TST); primary production/TST; consumption/TST; export/TST; and total biomass of the community. Large-scale differences were seen in the ecosystems of the Atlantic and Pacific Oceans, with the Western Atlantic being more complex with an increased ability to mitigate impacts, while the Eastern Atlantic showed lower internal complexity. In addition, the Eastern Pacific was less organised than the Eastern Atlantic although both of these systems had increased primary production as eastern boundary current systems. Differences by ecosystem type highlighted coral reefs as having the largest energy flow and total biomass per unit of surface, while lagoons, estuaries, and bays had lower transfer efficiencies and higher recycling. These differences prevailed over time, although some traits changed with fishing intensity. Keystone groups were mainly higher trophic level species with mostly top-down effects, while structural/dominant groups were mainly lower trophic level groups (benthic primary producers such as seagrass and macroalgae, and invertebrates). Keystone groups were prevalent in estuarine or small/shallow systems, and in systems with reduced fishing pressure. Changes to the abundance of key functional groups might have significant implications for the functioning of ecosystems and should be avoided through management. Conclusion/significance Our results provide additional understanding of patterns of structural and functional indicators in different ecosystems. Ecosystem traits such as type, size, depth, and location need to be accounted for when setting reference levels as these affect absolute values of ecological indicators. Therefore, establishing absolute reference values for ecosystem indicators may not be suitable to the ecosystem-based, precautionary approach. Reference levels for ecosystem indicators should be developed for individual ecosystems or ecosystems with the same typologies (similar location, ecosystem type, etc.) and not benchmarked against all other ecosystems.