Changes in land use have brought with them changes in plant cover, and over the last five hundred years the number of original natural ecosystems has dropped dramatically. However, deforestation was followed by the creation of a man-made mosaic of meadows, groves of trees, scrub-land and farmsteads that is both interesting and productive. Forestry plantations provide the predominant feature of the current landscape of the Biosphere Reserve, covering around 60% of its surface area.

25 different areas of vegetation can be distinguished in URDAIBAI in 8 more or less homogenous groups: five natural or spontaneous communities (leafy woods, scrub and flatlands, rocky outcrops, water plants and plants living on sandy coastal soil), and three in which human activity is essential to development and maintenance (forestry plantations, meadows and farmland/areas with vegetation that can be classed as cultivated). 615 species of vascular plants alone have been inventoried and described in the area.

Especially valuable are the area’s Cantabrian holm oak woods, which are the biggest coastal woods of their kind in the Basque Country. These evergreen trees are more usually found in a Mediterranean climate, and the woods also harbour a wide variety of other flora. They are dense and inaccessible, which has enabled numerous species of animals to thrive in them. They enjoy special protected status.

The rare, unusual plants found in the marshlands and the zoning by different units of flora that can be observed in URDAIBAI have earned the area international recognition. The river estuary also has special protected status under the URDAIBAI Protection Act.