The first ichthyofauna related studies in the lagoon were carried out in 1995. Of this group 12 species have been established. Later, several other species have been found. So far, 18 species have been described in the Atanasovsko lake, but it is likely that two of these species – Parablennius sanquinolenthus and carp, are no longer present.
Many of the fish species established in the lagoon are rare, temporary visitors and chance visitors coming from the sea. They exhibit different biological features. The three-spined stickleback and the atherine enter the lake from the sea. The Caucasian goby and the nine-spined stickleback are typical semi-saline water residents. The topmouth gudgeon, a typical fresh-water species, occurs only in the fresh-water marshes around the lake.
All fish species occurring in the Atanasovsko Lake lagoon are, due to their small size or numbers, not of economic interest to people. Some species such as the Caucasian goby, the topmouth gudgeon, the eastern mosquito fish and the three-spined stickleback occur in relatively high numbers and are some of the main food items of the large diversity of fish eating birds present in the lake.
The Caucasian goby is one of the most numerous fish species in the lagoon and occurs in all pools, except in the crystallizer pans. It is the most typical and constant inhabitant of the lake. It is a small fish, up to 5 g. in weight. Its body is spindle-shaped, with an oval head and distanced eyes protruding above the forehead of the fish. The species spawns between late May and late July, placing the caviar in sea shells or underneath stones. It is endangered with extinction and is listed in the Bulgaria's Red Data Book.

The Italian pipefish has been established in the Atanasovsko Lake only during the most recent years. It enters the sea during the summer and it is possible that some individuals breed in the lake. The species occurs in the pools in the northern part of the lake, overgrown by widgeongrass. This rare species is listed in the Bern Convention and in the IUCN Red List.
The eastern mosquito fish was acclimated in Bulgaria in 1924 as a mosquito-larva control measure. This fresh-water, viviparous species tolerates salinity of up to 7-8 ‰. In the lake, it occurs in the channel bypassing the northern salt pans.

The atherine is up to 13-14 cm long. Its other names are silver fish and gyumyush. It is a pelagic sea fish capable of sustaining large salinity fluctuations and regularly enters the rivers and lakes around the sea. Sea water is released into the lagoon in the early summer for salt production. Numerous schools of atherine are admitted with this water and feed in the lake. Being the subject of commercial fishing, the atherine has declined seriously during the recent years.
The Atanasovsko Lake ichthyofauna is highly vulnerable and dependent on the condition of this water body. Water pollution, change in salinity and the hydrological regime, the introduction of competing species and the destruction of breeding sites are some of the main threats for the various fish species.