Škocjanski zatok provides suitable living conditions for the following mammals:
- Brown Hare (Lepus europaeus)
- Southern White-breasted Hedgehog (Erinaceus concolor)
- Nutria (Myocastor coypus) – alochtone species
- Red Fox (Vulpes vulpes)
The remains of following small mammal species were found in the pellets of Barn Owl:
- Wood Mouse (Apodemus sylvaticus)
- Striped Field Mouse (Apodemus agrarius)
- Harvest Mouse (Micromys minutus)
- Black Rat (Rattus rattus)
- Brown Rat (Rattus norvegicus)
- Lesser White-toothed Shrew (Crocidura suaveolens)
- Bicolored White-toothed Shrew (Crocidura leucodon)
- Etruscan Shrew (also known as White-toothed Pygmy Shrew)(Suncus etruscus)