Currently, a central demand of coastal and marine food web researchers is the search for holistic and functional ecosystem health indicators. Based on concepts directly derived from R. L. Lindeman’s work (Lindeman 1942; Ecology 23:399–418), 6 estuarine food web models were analysed to assess the potential impact of multiple disturbances on the trophic state of food webs. The models described a Zostera noltii meadow and a bare sediment site in the Mondego estuary, Portugal, during 3 distinct time periods corresponding to (1) nutrient enrichment, (2) the implementation of mitigation measures, and (3) after a centenary flood. We tested 4 candidate metrics, directly derived from the trophic-dynamic concepts proposed by Lindeman (1942): food chain length, the detritivory/herbivory ratio, trophic efficiency per trophic level and mean trophic efficiency. Based on this case study, none of the metrics are yet ready to be used per se as operational metrics to quantify and interpret the impact of disturbances on the ecosystem’s trophic state. Trophic efficiency appeared to be sensitive to external pressures. However, the mean trophic efficiency of the system might not be sufficient to draw conclusions about the trophic efficiency of the ecosystem: trophic efficiency should be observed at the trophic level in order to better understand cascading effects within food webs.