During the past two decades, interest in inland water protection has increased, although the focus was primarily on lentic systems and selected wetland habitats. Biodiversity conservation, ranging from genetic diversity to landscapes, rarely targets rivers or streams in the Balkans. An exception is deltaic wetland areas. In fact, all the larger deltas contain protected areas such as Ramsar Sites, with statutory zonation designations. Human and natural factors are often deeply interdependent in these complex systems. The coastal lagoon systems, a priority habitat type for conservation in Europe, are usually exploited as traditional fish farms. Moreover, within the wider area of deltas, there are some unique habitats such as karstic ponds (deep cryptic depressions) either in marshes or in coastal lakes and lagoons, such as those encountered in the Neretva, Louros–Arachthos and Sperchios deltas. In the Sperchios upper delta, for example deep spring-fed ponds host the local endemic Pungitius hellenicus, perhaps the most range-restricted fish in the Balkans. Nonetheless, there are some upland riverine areas that have been assigned conservation status. These include some spectacular limestone gorges along the Nestos, Aoos, Arachthos and Alfeios, significant portions of the Axios, the virgin forests of Pirin (Nestos–Strymon basins) and Sredna Gora Mt (Evros basin) and several other headwater streams in the major river basins. Quite often, the main river channels are not included in conservation frameworks, and thus remain vulnerable to alteration.

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