Modification and loss of natural habitats caused by human activities are among the main drivers of biodiversity decline worldwide. To evaluate how land‐use changes affect species diversity at different spatial scales, amphibians represent an excellent group given that their complex life cycle requires both aquatic and terrestrial habitats. In this study, the influence of wetland characteristics and surrounding landscape features on richness and functional diversity of anurans was investigated in 26 natural wetlands in a human‐modified landscape within the Southern Andean Yungas. The analysis was performed at two spatial scales: wetland scale (the breeding pond structure) and the surrounding landscape scale. The classification of the landscape was limited to land uses modified by human activities within concentric circular buffers (radius = 0.1, 0.2, 0.5, and 1 km) centred on each breeding pond. Generalized linear models were applied to investigate the relationship between environmental variables measured at different scales and anuran species richness and functional diversity, respectively. Pond area best explained the observed variation in both diversity measures, which is consistent with other studies on anuran diversity in disturbed landscapes. In contrast to regression models including landscape scale variables only, integrated models (which included variables on both scales) highly improved model fit. Conservation strategies for anuran species diversity in these altered Andean Yungas forests should include efforts to maintain or restore aquatic habitats (e.g. breeding ponds) placed within suitable landscapes. Successful long‐term management will require an understanding of relationships between habitat characteristics at different spatial scales to identify variables that relate to species diversity in such heterogeneous habitats.