From 1996 19 species from 9 fish families have been recorded in the water bodies of Nature reserve Škocjanski zatok. Among them, at least 9 are considered as truly freshwater species.
The lis of the recorded fish species:
- Western Mosquitofish (Gambusia affinis)
- Mediterranean Killifish (Aphanius fasciatus)
- Golden Grey Mullet (Liza aurata)
- Thin-lipped Grey Mullet (Liza ramada)
- Leaping Grey Mullet (Liza saliens)
- Striped Mullet also known as Flathead Grey (Mugil cephalus)
- Thick-lipped Grey Mullet (Chelon labrosus)
- Three-spined Stickleback (Gasterosteus aculeatus aculeatus)
- Crucian Carp (Carassius carassius)
- Prussian Carp (Carassius gibelio)
- Roach (Rutilus rutilus)
- European Chub (Leuciscus cephalus)
- Rudd (Scardinius erythrophthalmus)
- Grass Goby (Zosterisessor ophiocephalus)
- Caucasian Dwarf Goby (Knipowitschia caucasica)
- European eel (Anguilla anguilla)
- Brown Bullhead (Ameiurus nebulosus)
- Big-scale Sand Smelt (Atherina boyeri)
- Atherina spp.
Invasive species are Western Mosquitofish and two freshwater species – Brown Bullhead and Prussian Carp – which were introduced to the Rižana River.
In 2011 a new research of fish in the lagoon of Škocjanski zatok was carried out aiming to provide an ichtiofaunistic overview of the lagoon a few years after its restoration. The results will soon be posted on the website.