Geographically isolated wetlands are critical biodiversity reservoirs, providing important habitat for plants, herpetofauna, and avifauna. Biodiversity monitoring is crucial to preserving imperiled species and communities of birds; however, most studies have relied only on species richness without recognizing the multi-scale and multi-component nature of biodiversity. The purpose of this study was to use the Measurement of Biodiversity (MoB) framework to examine changes in biodiversity and community composition of birds in geographically isolated wetlands distributed across pine savanna ecosystems at multiple spatial scales (α, β, and γ), using metrics that account for differences in abundance and sampling effort (rarefied richness (Sn) and evenness (SPIE)). Specifically, we tested if bird biodiversity was higher in geographically isolated wetlands compared to surrounding upland savannas (α-diversity), if the degree of spatial β-diversity was different within wetlands and uplands, and if community composition differed between wetlands and uplands. We conducted avian point count surveys of n = 18 wetlands and n = 6 uplands in 2021 and 2022, on two preserves with pine savanna habitats. We used direct ordination methods and linear mixed effect models to analyze differences in bird biodiversity and community composition in geographically isolated wetlands compared to surrounding uplands. We found that wetlands had significantly higher abundance (N), species richness (S), rarefied richness (Sn) and evenness (SPIE) than uplands at the α-scale. β-diversity was low in both wetland and upland habitats, and was not significantly different between habitats, indicating very little change in spatial β-diversity regionally within habitat types. Community composition varied primarily by habitat (wetland and upland), and secondarily by preserve. Geographically isolated wetlands are important repositories of bird biodiversity, and should be prioritized by land managers for their ecological value.