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The aim of this study was to compare estuarine food web network structure in the past, present and future, in a climate warming context, while also taking the trophic role of humans into account. Three versions of the Tagus Estuary (Portugal) food web were compiled representing its past (1970s), present (2000s) and future (2100s) trophic organization in relation to losses and gains of taxa and feeding links due to climate change. Although the species richness of the Tagus Estuary food web is expected to increase from past to present to future, along with links and mean links per species, due to a net gain of primarily fish species, there is little anticipated change in the structure of the food web. Unlike all but a few previously published food webs, the Tagus dataset explicitly includes humans, and compared to other predators in the food web, humans are supergeneralists that feed on an increasing fraction of available taxa from the past to the future, up to 38% of species by the 2100s. Such an increase in human impact results from many of the projected new species being commercial species in their current range. In addition, a supergeneralist shark, the milkshark Rhizoprionodon acutus, is predicted to enter the system in the future under climate change. Since the milkshark is likely to have a similar diet to humans, it may amplify the pressure on species already under fishing pressure and alter the function and stability of the Tagus estuary food web. Similar phenomena can occur at other mid-latitude estuaries.