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To understand how certain types of agroecosystem management provide resources for biodiversity and conservation opportunities beyond protected areas, it is necessary to consider the cumulative effects on a local scale. Our study focuses on a rice-Pantanal wetland agricultural system within Brazil, where our goals were: i) to quantify the impact of rice paddies on taxonomic, functional, and phylogenetic diversity metrics of small mammals as biodiversity indicators, ii) to compare diversity indices based on incidence and abundance data. We carried out a thorough assessment to sample small mammal species in both the rice paddy and the adjacent legal reserve by employing a multiple diversity metrics approach. We captured the small mammals until reaching saturation on the species accumulation curve over 12,774 trap nights, resulting in 447 individuals, 10 species, including seven rodents and three marsupial species. Abundance-based beta-diversity between rice-paddy and forest reserve were higher (0.95) than incidence-based estimate (0.33). The species composition differed between the legal reserve (8 spp.) and the rice paddy (7 spp.), with the reserve exhibiting higher taxonomic diversity values compared to the rice paddy. In terms of functional and phylogenetic diversity, overall, the rice paddy exhibited higher values for the incidence-based metrics and the abundance-based metrics indicated that the reserve was more diverse. We conclude that Neotropical Pantanal rice fields retain substantial functional and phylogenetic diversities, providing suitable habitats for species thriving in open and semi-aquatic environments. Simultaneously, the legal reserve retains an essential aspect of functional diversity, when considering abundance, needed to maintain ecosystem resilience and stability. Proper abundance estimation is thus a key parameter for accurately evaluating the role of agricultural landscapes as biodiversity conservation opportunities beyond protected areas. Abundance-based indices should be used to correctly evaluate the contribution of each habitat to agroecosystem sustainability, especially in seasonal or extreme event-prone environments.