The fish communities of the Mira estuary (Portugal) have been studied as a whole since 1986. It was possible to identify two different types of habitat that act as nursery areas and spawning grounds for a large number of fish species — the eel grass beds and the salt-marsh-bordered zone. The importance of these habitats is due, not only to the number of species present, but also to their abundance. However, as the eel grass beds only extend over a small surface in the Mira estuary, the salt marshes become of vital importance for the marine fish, especially those with economical value. As several major modifications are planned for the Mira estuarine bed and valley in the near future, suggestions are given in order to preserve the estuarine ecosystem equilibrium.