50 different species of breeding birds have been recorded at Škocjanski zatok Nature Reserve:
- Little Grebe (Tachybaptus ruficollis)
- Little Bittern (Ixobrychus minutus)
- Mute Swan (Cygnus olor)
- Mallard (Anas platyrhynchos)
- Garganey (Anas querquedula)
- Yellow-legged Gull (Phasianus colchicus)
- Water Rail (Rallus aquaticus)
- Moorhen (Gallinula chloropus)
- Common Coot (Fulica atra)
- Black-winged Stilt (Himantopus himantopus)
- Common Redshank (Tringa totanus)
- Little Ringed Plover (Charadrius dubius)
- Kentish Plover (Charadrius alexandrinus)
- Common Tern (Sterna hirundo)
- Little Tern (Sternula albifrons)
- Collared Dove (Streptopelia decaocto)
- Turtle Dove (Streptopelia turtur)
- Great Spotted Woodpecker (Dendrocopos major)
- Yellow Wagtail (Motacilla flava)
- Long-tailed Tit (Aegithalos caudatus)
- Rufous Nightingale (Luscinia megarhynchos)
- Blackbird (Turdus merula)
- Zitting Cisticola (Cisticola juncidis)
- Cetti’s Warbler (Cettia cetti)
- Great Reed Warbler (Acrocephalus arundinaceus)
- Blackcap (Sylvia atricapilla)
- Blue Tit(Cyanistes caeruleus)
- Great Tit(Parus major)
- Common Starling (Sturnus vulgaris)
- Magpie(Pica pica)
- Tree Sparrow (Passer montanus)
- House Sparrow (Passer domesticus)
- European Serin (Serinus serinus)
- Greenfinch (Carduelis chloris)
- Goldfinch (Carduelis carduelis)
- Hooded Crow (Corvus (corone) cornix)
- Reed Warbler (Acrocephalus scirpaceus)
- Melodious Warbler (Hippolais polyglotta)
- Common Pochard (Aythya ferina)
- Great Crested Grebe (Podiceps cristatus)
- Wryneck (Jynx torquilla)
- Spotted Flycatcher (Muscicapa striata)
- Barn Swallow (Hirundo rustica)
- Pheasant (Phasianus colchicus)
- Collared Dove (Streptopelia decaocto)
- Purple Heron (Ardea purpurea) – breeding species since 2017!
- Greylag Goose (Anser anser) breeding species since 2018!
- Wood pigeon (Columba palumbus) breeding species since 2019!
- Eurasian golden oriole (Oriolus oriolus) – breeding species since 2019!
- Pied avocet (Recurvirostra avosetta) – specie nidificante dal 2019
