Intensification of agriculture has led, among other negative consequences, also to drying out of wetlands. Nevertheless, some of the wetland biotopes were preserved as small spots. This paper discusses the importance of those areas serving as refugia for small terrestrial mammals. Because small terrestrial mammals in the middle of food webs, they serve as an indicator for the presence of food sources (plants and invertebrates) and suggest the potential of the area as a living space for predators. The experiment took place at lowland agricultural landscape with wetland patches in west and west-east Slovakia (Záhorská and Podunajská nížina lowlands) using catch-mark-release method from 2015 to 2017. The importance was assessed according to abundance, biodiversity, persistence of species during seasons and habitat preference of small terrestrial mammals and equitability of the biotopes. Overall 368 individuals belonging to 12 species were recorded. The lowest abundance and diversity were registered at field biotopes where Apodemus sylvaticus was the most abundant. Microtus arvalis, Clethrionomys glareolus and Sorex araneus dominate at wetland biotopes. The higher biodiversity and abundance of small mammals were recorded at the wetland refugia. The results, together with position of small mammals in food webs, lead to conclusion that the wetland refugia are important habitats for the overall preservation of biodiversity and maintaining them is a part of the strategy for sustainable agriculture.