Dinaric karst water systems support 25% of the total of 546 fish species in Europe. Watercourses of this area support a large number of endemic species of fish. The river Neretva and its tributaries represent the main drainage system in the east Adriatic watershed and the foremost ichthyofaunal habitat of the region. According to Smith & Darwall (2006) the Neretva River, together with four other areas in the Mediterranean, has the largest number of threatened freshwater fish species.
The degree of endemism in the karst ecoregion is greater than 10% of the total number of fish species. Numerous species of fish that inhabited this area live in very narrow and limited areas and are vulnerable, so they are included on the Red List of endangered fish and the IUCN-2006. The Adriatic basin has 88 species of fish, of which 44 are Mediterranean endemic species, and 41 are Adriatic endemic species. More than half of the Adriatic river basin species of fish inhabit the Neretva, the Ombla, the Trebišnjica, the Morača Rivers and their tributaries, and more than 30 are indigenous.
The Neretva river with its many tributaries, lakes and marshes provides rich freshwater habitat for its native, as well as for introduced non-native fish species. Depending on the location along the rivers, there can be deep canyon as well as wide valley sections with both fast flowing rapids with side-pools, and narrow section with deep, still waters running slowly. The flowing water can be any combination of fast or slow, deep or shallow, open or protected by canyons, rocks, tree roots and undercut banks, and shaded by vegetation on the bank or exposed to full sunlight. This variation ensures that a relatively large number of fish species are able to find suitable habitat for themselves. Upper reaches of the Neretva basin (Upper Neretva), river with its tributaries runs undisturbed through remote and rugged limestone terrain with deep canyons and steep slopes gorges reaching from 600 to 1200 m in depth. River in these parts is extremely cold, clear and potable, consisting waters of "Class I" ("Class A") purity, with temperature often as low as 7–8 degrees Celsius in the summer months, evidence of almost certainly the coldest river water in the world. In the middle section of the watershed remoteness and ruggedness of the terrain gets even more extreme, especially around small river tributaries, mountain creeks and lakes, however the Neretva river itself is completely flooded throughout entire mid-section with 4 large artificial lakes, and intersected with 4 large dams. More downstream in the lower reaches (Lower Neretva), the Neretva basin and the river itself comprise remarkable landscape, in which valley from the confluence of its main tributaries of the section, the Buna, the Trebižat and Bregava rivers, then spreads into an alluvial fan, covering more then 20,000 hectares, with specious flat plains or polje's, where water-flow is slow but abundant, with many branches often widened into natural lakes and marshes, and constantly replenish with lots of fresh water from numerous large karstic well-springs. Finally at the Neretva Delta, river reach the Adriatic Sea.
Spotted Minnow(Bosnian: Gaovica) (Phoxinellus adspersus), endemic to Bosnia and Herzegovina and Croatia. This species is present in the Tihaljina River, which is fed by underground waters from Imotsko field and is connected to the Trebižat River via the Mlada River, and also occurs in Mostarsko Blato wetlands. Fish were found in the source of the Norin River, a right-hand tributary of the lower Neretva at Metković, in Croatia, at Kuti Lake, a left-hand tributary of the lower Neretva, at Imotsko field in Crveno Lake and the Vrljika River drainage and near Vrgorac in the Matica River system. It is considered vulnerable.
Neretvan Nase (also Dalmatian Nase and Dalmatian Soiffe) (Bosnian: Neretvanska podustva) (Chondrostoma knerii) is a fish species endemic to the Neretva River. Neretvan Nase is mainly distributed in the lower parts and delta of the Neretva River shared between Croatia and Bosnia and Herzegovina, the river's left tributary Krupa River, Nature Park Hutovo Blato wetlands, and Neretva Delta wetlands. It occurs in water bodies with little current. It is threatened by habitat destruction and pollution. It is considered Vulnerable (VU).
Adriatic Dace also Balkan Dace (Bosnian: Strugač or Sval) (Squalius svallize also Leuciscus svallize Heckel & Kner 1858) endemic to Bosnia and Herzegovina and Croatia, also to Montenegro and Albania. Adults inhabit water bodies on the low plains, with little current and in lakes. They feed on invertebrates. It is threatened due to pollution, habitat destruction and due to introduction of other species. It is considered vulnerable.
Illyrian Dace(Bosnian: Ilirski klijen) (Squalius illyricus also Leuciscus illyricus Heckel & Kner 1858) inhabits karstic waters of Bosnia and Herzegovina, Croatia and Albania. It occurs in water courses on low plains, with little current. It feeds on invertebrates. It is threatened due to habitat destruction, pollution and the introduction of other species. It is considered Near Threatened (NT).
Turskyi Dace(Bosnian: Turski klijen) (Leuciscus turskyi also Squalius turskyi turskyi and Telestes turskyi) inhabits karstic waters, Lake Buško Blato in Bosnia and Herzegovina and the Krka and Čikola Rivers in Croatia. It occurs in water courses on the low plains, with little current and in lakes. It feeds on invertebrates. It is threatened due to water abstraction and pollution. It is considered Critically Endangered (CR).
Neretvan Spined Loach (Bosnian: Neretvanski vijun) (Cobitis narentana Karaman, 1928) is an Adriatic watershed endemic fish that inhabits a narrow area of the Neretva watershed in Croatia and Bosnia and Herzegovina (Mrakovčić et al., 2006). In Bosnia and Herzegovina it inhabits only the downstream of the Neretva River and its smaller tributaries like the Matica River. In CroatiaNeretvanski vijun is a strictly protected species and inhabits only the Neretva delta and its smaller tributaries, the (Norin) and lake systems of the Neretva delta (Baćina lakes, Kuti, Desne, Modro oko) (Mrakovčić et al., 2006). It is considered Vulnerable (VU).
The ichthyofauna of the Neretva delta is rich in endemic species, and there are more than 20 endemic species, of which 18 species are endemic species of the Adriatic watershed, and three endemic species in Croatia. Nearly half (45%) of the total number of species that inhabit this area are included in one of the categories of threat, and are mainly endemic species.
Sander also Pike Perch (Bosnian: Smuđ) (Sander lucioperca Linnaeus 1758) (also see Sander) population in the Neretva River watershed was observed in 1990 for the first time. It was the Rama river, a right tributary of the Neretva, and its Rama Lake that received an unknown quantity of this allochthonous species. Analyzing the results of the research, there are a tendency to increase the quantity of Pike Perch in the Neretva accumulation lakes. This fact confirms previous scientific assumptions of Škrijelj (1991, 1995), who predicted the possibility of Pike Perch displacement (fish migration) from Ramsko Lake to the Rama river (a right tributary of the Neretva), and then further downstream to the river and its lakes.
In 1990 the Perch population made up 1.95% of the fish population in Ramsko Lake. Within a decade this rose to 25.42% in a downstream nearby Jablaničko Lake.
On the basis of analysis of the obtained data, it can be concluded that the populations of the allochthonous species Pike Perch causes clearly visible negative effects on the autochthonous ichthyofauna in Jablaničko Lake; on autochthonous ichthyofauna of artificial Salakovačko Lake these effects are in progress and less visible, while the population of Perch is in the initial phase of adaptation to existing conditions in Grabovičko Lake and currently not yet clearly visible.
Taking the fact that the introduction of the Pike Perch has a substantial impact on the diversity of autochthonal ichthyofauna as a starting point, the population of this species in the Neretva River reservoirs (Jablaničko Lake, Grabovičko Lake and Salakovačko Lake) was investigated. Based on the results of the investigation of the Perch population in the Neretva river “lakes”, it can also be concluded that it is growing with a tendency of spreading across the Neretva river basin of the Adriatic Sea in Bosnia and Herzegovina.
On the basis of all relevant indicators it is necessarily to take urgent measures, continuous and organized action, to dramatically reduce the quantity (if is not possible to exterminate) of this allochthonous type of fish, as well as to attempt to revitalize autochthonal fish populations, with fish stocking of local, especially salmonids species, all in order to prevent the same fatal experience with the water ecosystem in the UK, and prevent, if possible, this type of allochtonous species colonization of the Neretva River basins with irreversible effects.
Like in many rivers around Europe, there are some introduced salmonid fish species in the Neretva too. Luckily only grayling (Thymallus thymallus) established stable population so far, while more harmful rainbow trout (Oncorhynchus mykiss) had less successful survival rate and accordingly low population growth and small size. Brook trout (Salvelinus fontinalis) and lake trout (Salvelinus namaycush) are both recent addition to almost all of the Neretva basin reservoirs, fortunately with moderate to low success in establishing stable populations. At least for now populations of these invasive salmonids are rather weak.