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 One of the main characteristics of this enclave is its ecological diversity, both in terms of habitats and in terms of species, all of which is perfectly reflected in its various communities of birds. In fact, even though all the ecosystems are within the same physical territory and are interrelated with each other, each one of them maintains their own well-defined identity.
In the most exterior part of the estuary, there is a predominance of a marine environment, with coastal cliffs, important sandy areas (Laga and Laida) and Izaro Island. The particular terrain of coastal cliffs, with the presence of numerous caves and shelves that are inaccessible for the human being, shelters a very selective and original nesting community of marine birds, where yellow-legged gulls (Larus cachinnans) are predominant but on which shags (Phalacrocorax aristotelis) and storm petrels (Hydrobates pelagicus) are especially noteworthy. Cape Ogoño contains the best representation of coastal cliffs, counting, besides, with the presence of other less specialised but undoubtedly interesting species like peregrine falcons (Falco peregrinus) or blue rock thrushes (Monticola saxatilis). However, Izaro Island takes advantage of its insularity to concentrate the most numerous colonies of marine birds. Recently, the new nesting colony of little egrets (Egretta garzetta) has been identified.
This is a species that habitually uses this island as a place in which to spend winter.
 During winter, and especially during migrations, the close and the mouth of the estuary receive a great quantity of marine birds that fly in from Europe, including gannets, shearwaters, skuas, sea ducks, terns, divers, and various species of gulls. Many of these birds, when there are storms or strong winds, use the inside of the estuary to seek protection, and thus their observation is far easier.
However, the most characteristic ecosystem of the estuary is its ample intertidal lime and sand surfaces, that offer some good opportunities for the development of some very diverse communities of invertebrates, especially including bivalves, gastropods and bristleworms. This resource is shared by the traditional human use of "sea food fishing" and by water fowl, that have a group that is specialised in its exploitation: the wading birds. These birds are especially numerous in winter and particularly so during migrations. Especially noteworthy because of their abundance are the dunlins (Calidris sp.), curlews (Numenius sp.), redshanks (Tringa sp.), godwits (Limosa sp.), plovers (Pluvialis sp) and oystercatchers (Haematopus ostralegus). During those same dates, on the shores of canals or open intertidal areas it is possible to observe herons and egrets, amongst which spoonbills (Platalea leucorodia) stroll placidly. Spoonbills are an authentic ornithological jewel, the observation of which greatly depends on the wetlands it uses during its migration, and the Gernika estuary is one of its favourite resting places. This issues takes advantage of its long legs to walk around shallow areas of the estuary filtering the water in search for the necessary food to complete its migration, which takes place every season between the Netherlands and the wetlands of the north of Africa.
In more interior areas of the estuary, taking advantage of the former riverbed and the lesser influence of the sea, we find patches of wild reeds (Phragmites australis) and bulrushes (Typha latifolia). This habitat, that has good redoubts in Fórua and Kortezubi, also has some specialised birds, amongst which especially noteworthy are reed warblers (Acrocephalus scirpaceus), great reed warblers (Acrocephalus arundinaceus) and water rails (Rallus aquaticus). Besides, in the estuary environment we find a landscape in a good state of conservation with a considerable sheltering capacity for paseriform, and which is used also by lawpings (Vanellus vanellus), golden plovers (Pluvialis apricaria), curlews (Numenius arquata) and snipes (Gallinago gallinago), especially when the phreatic level is near the surface, as is usually the case in fields and some polders.
Besides, to the value that the Gernika estuary undoubtedly has because of its ornithological diversity and presence of threatened birds, it is necessary to add its important role as a refuge for birds during the waves of polar cold that sometimes cross Europe. In these conditions, there can be impressive concentrations of birds in the estuary and its surroundings, the survival of which depends on the good state of conservation that we are able to maintain in this special enclave.
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