Freshwater wetlands are rapidly declining due to the expansion of agriculture and urbanisation, resulting in significant biodiversity loss. In the Swiss lowlands, 90% of wetlands have been lost. Researchers and farmers are therefore jointly exploring the pesticide-free cultivation of paddy rice as a land-sharing approach that increases habitat availability for aquatic organisms. We studied the role of rice paddies for aquatic biodiversity by comparing key environmental variables and macroinvertebrate communities with those in nearby natural wetlands over a 2-year period. Rice paddies may provide a more uniform aquatic environment than natural wetlands. Accordingly, wetlands harboured a higher taxon richness at the regional scale, but at the local scale, macroinvertebrate density and richness were higher in rice paddies (1212 [95% CI: 714–2058] vs. 448 [263–761] ind./m2 and 19.36 [17.36–21.59] vs. 13.39 [11.90–15.08] taxa/site, respectively). In contrast, Shannon diversity was higher in wetlands than in rice paddies (1.69 [1.51–1.87] vs. 1.46 [1.27–1.64]). Six rice paddies were constructed with a deeper side ditch, which may provide a distinct habitat element promoting additional taxa, but its overall effect on rice paddy communities was limited. These results highlight the ecological value of rice paddies in providing large areas of temporary habitat for freshwater species that can complement but not replace natural wetlands in Swiss agricultural landscapes. While they show some parallels to studies from warmer rice-growing regions, our findings mainly apply to cold-temperate climate and pesticide-free cultivation, stressing the importance of effective management practices to maximise the ecological benefits of rice paddies.