Migratory species are non-breeding birds which winter in the area only in exceptional cases or in small numbers. In a much larger numbers they occur during the spring (from mid-February to mid-May) and autumn migration (mid-July to mid-November). In the spring, the birds are returning to their nesting grounds from the areas further south where they were wintering while in the autumn, after nesting are again migrating to the south. 89 species of recorded birds in Škocjanski zatoku are clasified to this category.
The list of migratory species:
- Black-necked Grebe(Podiceps nigricollis)
- Red-necked Grebe (Podiceps grisegena)
- Night Heron (Nycticorax nycticorax)
- Cattle Egret (Bubulcus ibis)
- White Stork (Ciconia ciconia)
- Black Stork (Ciconia nigra)
- Eurasian Spoonbill (Platalea leucorodia)
- Glossy Ibis (Plegadis falcinellus)
- Pintail (Anas acuta)
- Ferruginous Duck (Aythya nyroca)
- Red Kite (Milvus milvus)
- White – tailed Eagle (Haliaeetus albicilla)
- Short-toed Eagle (Circaetus gallicus)
- Marsh Harrier (Circus aeruginosus)
- Montagu‘s Harrier (Circus pygargus)
- Hobby (Falco subbuteo)
- Red-footed Falcon (Falco vespertinus)
- Common Quail (Coturnix coturnix)
- Spotted Crake (Porzana porzana)
- Little Crake (Porzana parva)
- Avocet (Recurvirostra avosetta)
- Great Ringed Plover (Charadrius hiaticula)
- European Golden Plover (Pluvialis apricaria)
- Grey Plover (Pluvialis squatarola)
- Sanderling (Calidris alba)
- Red Knot (Calidris canutus)
- Curlew Sandpiper (Calidris ferruginea)
- Dunlin (Calidris alpina)
- Little Stint (Calidris minuta)
- Temminck’s Stint (Calidris temminckii)
- Ruff (Philomachus pugnax)
- Whimbrel (Numenius phaeopus)
- Black-tailed Godwit (Limosa limosa)
- Bar-tailed Godwit (Limosa lapponica)
- Spotted Redshank (Tringa erythropus)
- Marsh Sandpiper (Tringa stagnatilis)
- Wood Sandpiper (Tringa glareola)
- Green Sandpiper (Tringa ochropus)
- Great Snipe (Gallinago media)
- Gull-billed Tern (Gelochelidon nilotica)
- Black Tern (Chlidonias niger)
- White-winger Black Tern (Chlidonias leucopterus)
- Whiskered Tern (Chlidonias hybridus)
- Wood Pigeon (Columba palumbus)
- Stock Dove (Columba oenas)
- Common Cuckoo (Cuculus canorus)
- European Nightjar (Caprimulgus europaeus)
- Alpine Swift (Tachymarptis melba)
- European Bee-eater (Merops apiaster)
- Hoopoe (Upupa epops)
- Wryneck (Jynx torquilla)
- Wood Lark (Lullula arborea)
- Sand Martin (Riparia riparia)
- Red-rumped Swallow (Hirundo daurica)
- Tree Pipit (Anthus trivialis)
- Thrush Nightingale (Luscinia luscinia)
- Bluethroat (Luscinia svecica)
- Common Redstart (Phoenicurus phoenicurus)
- Whinchat (Saxicola rubetra)
- Northern Wheatear (Oenanthe oenanthe)
- Redwing (Turdus iliacus)
- Song Thrush (Turdus philomelos)
- Grasshopper Warbler (Locustella naevia)
- Savi’s Warbler (Locustella luscinioides)
- Moustached Warbler (Acrocephalus melanopogon )
- Icterine Warbler (Hippolais icterina)
- Lesser Whitethroat (Sylvia curruca)
- Garden Warbler (Sylvia borin)
- Common Whitethroat (Sylvia communis)
- Barred Warbler (Sylvia nisoria)
- Subalpine Warbler (Sylvia cantillans)
- Sardinian Warbler (Sylvia melanocephala)
- Willow Warbler(Phylloscopus trochilus)
- Wood Warbler (Phylloscopus sibilatrix)
- Firecrest (Regulus ignicapillus)
- Pied Flycatcher (Ficedula hypoleuca)
- Collared Flycatcher (Ficedula albicollis)
- Golden Oriole (Oriolus oriolus)
- Lesser Grey Shrike (Lanius minor)
- Woodchat Shrike (Lanius senator)
- Siskin (Carduelis spinus)
- Common Crossbill(Loxia curvirostra)
- Black-headed Bunting (Emberiza melanocephala)