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While artificial farmland drainage has allowed the development of a highly productive agriculture, the availability of periodically flooded arable land as a niche habitat for a broad range of animal and vascular plant species has diminished. Accordingly, many species depending on temporary wetlands are endangered, already extinct or extirpated in Switzerland and other European countries. Some arable fields with temporary pools can still be observed in Switzerland. However, it is not known how suitable such small temporary ponds are as habitats in the modern, intensively-managed agricultural landscape, where disturbance rates are high, and connecting wetland habitats are scarce. We surveyed 120 fields across 10 hot spot regions for potential waterlogging in Switzerland, investigating the effect of temporary waterlogging on the diversity of arable plant and ground beetle species. Half of the fields were heavily influenced by waterlogging, while the other half represented conventional crop field controls. We found that wet fields exhibited a higher number of vascular plant and carabid species on average compared to control fields. This difference was explained by the presence of more hygrophilic plant and ground beetle species on wet fields. While we did find more hygrophilic species on wet fields, the threatened character species of temporary wetland habitats were mostly absent despite availability in regional species pools. These results suggest that temporary pools still provide the raw environmental characteristics that hygrophilic species require in the agricultural landscape. However, alternative management schemes are required to transform them into habitats that can effectively support high-priority, threatened species of temporary wetlands.