The role of rice fields as refuges for wetland macroinvertebrates was assessed at multiple spatial scales, and macroinvertebrate diversity was compared between fields and natural wetlands. Because irrigated rice fields are highly disturbed environments, and have lower environmental complexity and heterogeneity in the irrigated phase than do wetlands, we hypothesised that the fields would sustain lower diversity than do wetlands, especially at broader spatial scales. Wetlands and rice fields from three regions in southern Brazil were simultaneously sampled. In wetlands, the broadest scale (hydrographic basin) contributed the most to macroinvertebrate diversity. In rice fields, besides hydrographic basin level, narrower scales (site level) also contributed to macroinvertebrate γ diversity. Different cultivation and management systems may be responsible for the contribution of narrower scales to γ diversity in rice fields. Differences in community structure in both environments were determined by wetland drainage practices, and they were affected by the ENSO climatic phenomenon, which influenced macrophyte diversity in wetlands. Wetland communities were characterised by macrophyte-associated, passive-dispersing taxa, whereas rice fields contained short-lived, active-dispersing macroinvertebrates. The present study demonstrated that rice fields do not represent suitable refugia for wetland-expelled macroinvertebrates because they do not support similar community structure, at least under some management practices and climatic conditions influenced by ENSO.