Mondego Estuary represents the last stage of this river since it starts at Estrela Mountain. In this sector a number of important aquatic habitats harbour an interesting diversity of birds. Of these places, the Special Protection Area of Paul do Taipal, in Montemor-o-Velho, stands out. In this wetland we can find several species of ducks. Shoveler Duck (Anas clypeata), the Pintail (Anas acuta), the Mallard Duck (Anas platyrhynchos) and the Common Teal (Anas crecca). The Marsh Harrier (Circus aeruginosus), a species present throughout the year, constantly patrols the reeds in search of surprising an unsuspecting prey. Also here we can find the Glossy Ibis (Plegadis falcinellus), the Coot (Fulica atra) and the rare Purple Swap-hen (Porphyrio porphyrio).

Continuing the course towards the mouth, in Figueira, the Island of Murraceira, an area of ​​estuary and salt pans, the diversity and quantity of waders is considerable. Here, large numbers of herons and wading birds congregate every winter, such as the Little Egret (Egretta garzetta), the Great Egret (Ardea alba), the Grey Heron (Ardea cinerea), the Black-winged Stilt (Himantopus himantopus), the Avocet (Recurvirostra avosetta) and the Ruff (Philomachus pugnax). But the highlight goes to the beautiful flamingos (Phoenicopterus roseus), the peculiar spoonbills (Platalea leucorodia), the unique Osprey (Pandion haliaetus) and the elusive Short-eared Owl (Asio flammeus). Still in winter, it is also possible to see a couple of Black Storks (Ciconia nigra) and, hiding in the reeds, some bluethroats (Luscinia svecica).