The intensification of agriculture over the last few decades has caused habitat loss, which poses a significant threat to the survival of populations and species. Where habitats are connected, populations may escape the destruction of their habitat by migrating to another one. Consequently, the functional connectivity of landscapes has become an important focus for species conservation. Kettle holes are hotspots of biodiversity that provide suitable conditions for wildlife species (i.e., amphibians, insects, aquatic plants) and contribute to landscape heterogeneity. They are also considered to function as stepping stone habitats that contribute to habitat connectivity. This study assesses the contribution of kettle holes for (i) habitat provision and (ii) the functional connectivity of three amphibian species with different movement ranges, and (iii) the study identifies areas where the creation of stepping stone biotopes could improve functional connectivity. The contribution of kettle holes was assessed using GIS-based clustering within three research areas in Germany. It was found that the importance of kettle holes for providing amphibian habitats in the three studied areas was equal to or higher than that of other wetland habitats. The state of functional connectivity and the contribution of kettle holes differed strongly depending on the species’ range. For the short-range species, landscapes were highly fragmented, and the contribution of kettle holes was much smaller than that of corridor habitats. For the long-range species, all habitats suited for amphibian reproduction were connected, and the contribution of kettle holes was similar to that of corridor habitats. However, the contribution of both was mostly redundant. Overall, the results showed that kettle holes play a crucial role in habitat provision and function as important stepping stone biotopes in agricultural landscapes. The clustering method applied in this study provides a simple tool for landscape planning and environmental protection agencies, which can be easily adapted to analyze functional connectivity and habitat interactions for different species or landscapes.