Lagoons may be primary (storm-beaches, wave-eroded coasts) or secondary (separated from the sea by flood banks or sluice gates). The mouths of rivers/streams should be recorded as estuaries (1130), even if they are separated from the sea by storm beaches. They differ from lagoons in that they are continuously influenced by freshwater.

Standing waterbodies which are more or less regularly reached by sea water during storm tides are to be recorded. The seawater influence can be direct, or indirect by way of underground flow through the seaward barrier. Apart from this intermittent influence, the continuous ingression of low volumes of seawater can lead to comparable hydrological situations. The degree of seawater influence can generally be deduced from the occurrence of the respective halophytic vegetation. Standing waterbodies which contain only freshwater should not be included in this category.

In the Baltic there are extensive and in part richly structured Bodden and Bodden parts which on account of their character can be assigned to the Coastal lagoons habitat type provided they fulfil the following criteria:

• largely or clearly separated from the sea,
• no defining freshwater ingression from landward tributaries

The Bodden include estuaries, shallow inlets and bays, and lagoons.

The habitat type should be delimited using the mean water tide. It thus includes the waterbody as well as the shorelines with their reed swamps, tall herbaceous perennial vegetation, and pioneer communities. Adjacent terrestrial sites do not belong into this category even if they are occasionally flooded. However, the latter should for functional reasons be included in the site delimitation for the purposes of Natura 2000.