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The Little Tern has a fairly restricted distribution only in eastern Europe, while its range is very fragmented elsewhere and almost non-existent in northern Europe. In Slovenia, it breeds exclusively on the coast, only in the Sečovlje salt pans and the Škocjanski bay Nature Reserve.

It started nesting in the Sečovlje salt pans in 1985 and no more than three pairs have nested there for more than ten years. Only in 2002 more than ten pairs nested, in 2005 more than 20 pairs and in 2012 as many as 72 pairs. Subsequently, the population declined, with fewer than 30 pairs nesting in 2016. Little Terns nest colonially on sandy and pebbly sea shores, in salt marshes, on islands, as well as on the shores of lakes and large inland rivers. In the Sečovlje salt pans, it nests in small, scattered colonies on the banks of larger pools, low unvegetated embankments, small mud islands or fossil beds in the middle of larger salt pans, choosing soils with little or no vegetation and modestly lining the nest with snail and mussel shells. In the Sečovlje salt pans, 12-72 pairs of Little Terns nested in an area of 47 ha in the period 2002-2015, which translates into a density of 0.3-1.5 pairs/ha.

There is no known trend in Little Tern conservation in Europe, but globally it is declining. As the Little Tern prefers to nest in the lowest, almost level areas, its breeding success is often low due to nest waterlogging. In the Sečovlje salt pans, it is also threatened by inadequate water levels due to weather conditions (heavy rainfall, which causes eggs to stick to the substrate and collapse) and inadequate management of the water regime for salt production (poor control of water levels, dilapidated infrastructure), predation (grey crow, magpie, fox), walkers and inappropriate forms of recreation (bathing, smearing with salt mud). Active salt farming, which ensures dykes and appropriate water regimes, supports the conservation of the Little Tern. The proposed conservation measures for the species are adequate water levels in areas of interest for breeding and maintenance of an appropriate water regime.

*The Sečovlje Salt Pans is considered a qualifying species in favourable conservation status.