The Mondego estuary (Portugal) has suffered severe ecological stress over the last two decades, as manifested in the replacement of seagrasses by opportunistic macroalgae, degradation of water quality and increased turbidity. A restoration plan was implemented in 1998, which aimed to reverse the eutrophication effects, and especially to restore the original natural seagrass (Zostera noltii) community. This article explores the long-term changes in Ampithoe valida and Melita palmata (Amphipoda) populations in response to eutrophication (with consequent seagrass loss and macroalgal proliferation) and to the subsequent restoration plan (with progressive seagrass recovery and macroalgal biomass decline). Until the early 1990s, high densities of A. valida and M. palmata were recorded in the Mondego estuary, especially during the occurrence of the macroalgal bloom and during all the periods in which green macroalgae were available. After the implementation of the restoration plan, species abundance, biomass and production levels decreased considerably due to the progressive decline of green macroalgae. This implied the virtual disappearance of the amphipod population, mainly A. valida. Distinct behaviours displayed by the two species could be related to different food strategies and habitat preferences. Ampithoe valida showed feeding preferences for ephemeral softer, filamentous or bladed algae (e.g. Ulva sp.) due to its high caloric content, using the Z. noltii bed only as a habitat for protection against predators or shelter from wave action. On the other hand, M. palmata did not suffer a strong decline in its population density, biomass and production, which may indicate that this species is probably not a primary consumer of green macroalgae and may readily shift to alternative ecological niches.