This is a list of Estonian fish. Native (usually synonymous with indigenous) species are considered to be species which are today present in the region in question, and have been continuously present in that region since a certain period of time. There are no endemic fish species in Estonia (that is, there are no fish species native to only this region).

• Sea lamprey, Petromyzon marinus
• European river lamprey, Lampetra fluviatilis
• Brook lamprey, Lampetra planeri

• European sea sturgeon, Acipenser sturio

• Atlantic herring, Clupea harengus membras
• European sprat, Sprattus sprattus balticus
• Twait shad, Alosa fallax

• European anchovy, Engraulis encrasicholus

• Atlantic salmon, Salmo salar
• Brown trout, Salmo trutta
  • Brown trout (riverine form), Salmo trutta morpha fario
• Rainbow trout, Oncorhynchus mykiss
• Vendace, Coregonus albula
• Northern whitefish, Coregonus peled
• Common whitefish Coregonus lavaretus
  • Coregonus lavaretus maraenoides
• Grayling, Thymallus thymallus

• European smelt Osmerus eperlanus
  • Osmerus eperlanus morpha spirinchus

• Northern pike Esox lucius

• European eel Anguilla anguilla

• Roach, Rutilus rutilus
• Common dace, Leuciscus leuciscus
• European chub, Leuciscus cephalus
• Ide, Leuciscus idus
• Eurasian minnow, Phoxinus phoxinus
• Rudd, Scardinius erythrophthalmus
• Asp, Aspius aspius
• Moderlieschen, Leucaspius delineatus
• Tench, Tinca tinca
• Gudgeon, Gobio gobio
• Bleak, Alburnus alburnus
• Spirlin, Alburnoides bipunctatus
• Silver bream, Blicca bjoerkna
• Carp bream, Abramis brama
• Zarte, Vimba vimba
• Ziege, Pelecus cultratus
• Crucian carp, Carassius carassius
• Prussian carp, Carassius gibelio
• Common carp, Cyprinus carpio
• Grass carp Ctenopharyngodon idella
• Bighead carp Aristichthys nobilis

• Cobitis taenia
• Weatherfish Misgurnus fossilis

• Stone loach Barbatula barbatula

• Wels catfish Silurus glanis

• Channel catfish Ictalurus punctatus

• Garfish, Belone belone

• Burbot, Lota lota
• Pollock, Pollachius pollachius
• Atlantic cod, Gadus morhua callarias

• Four-bearded rockling Rhinonemus cimbrius

• Three-spined stickleback, Gasterosteus aculeatus
• Nine-spined stickleback, Pungitius pungitius
• Fifteen-spined stickleback, Spinachia spinachia

• Straightnose pipefish, Nerophis ophidion
• Deepnosed pipefish, Syngnathus typhle

• Zander, Sander lucioperca
• European perch, Perca fluviatilis
• Eurasian Ruffe, Gymnocephalus cernuus

• Snake blenny, Lumpenus lampetraeformis

• Butterfish, Pholis gunnellus

• Viviparous eelpout, Zoarces viviparus

• Lesser sand eel, Ammodytes tobianus
• Great sandeel, Hyperoplus lanceolatus

• Black goby, Gobius niger
• Sand goby, Pomatoschistus minutus
• Common goby, Pomatoschistus microps
• Twospotted goby, Coryphopterus flavescens
• Neogobius melanostomus

• Atlantic mackerel, Scomber scomber

• Swordfish, Xiphias gladius

• Fourhorn sculpin, Triglopsis quadricornis
• Father Lasher, Myoxocephalus scorpius
• Long-spined Sea Scorpion, Taurulus bubalis
• European bullhead, Cottus gobio

• Lumpsucker, Cyclopterus lumpus

• Snailfish, Liparis liparis

• Turbot, Scophthalmus maximus

• Common dab, Limanda limanda
• European plaice, Pleuronectes platessa
• European flounder, Platichtys flesus trachurus

• E. Ojaveer, E. Pihu, T. Saat. Fishes of Estonia, 2003.