ABSTRACT Subterranean waters are important but understudied biodiversity reservoirs, particularly in the semi‐arid Caatinga biome. We quantified the biological uniqueness of zooplankton communities in these groundwater‐dependent systems and investigated how environmental conditions shape beta diversity. We sampled 12 subterranean aquatic ecosystems (ponds, lakes, rivers, and springs) over 3 years. We computed local contributions to beta diversity for species composition (LCBD) and environmental heterogeneity (LCEH), related LCBD to LCEH and richness, quantified species contributions to beta diversity (SCBD), compared community composition among habitats, seasons and ecosystem types, and tested for distance–decay patterns in community dissimilarity. Environmentally distinctive sites (high LCEH) harboured more compositionally unique communities (higher LCBD) with fewer taxa. Compositional uniqueness increased with total phosphorus, indicating that nutrient‐enriched sites supported more distinctive, low‐richness assemblages, with guano‐influenced ponds in Furna Feia cave being the most environmentally and biologically unique. K‐like taxa (copepods and lobose testate amoebae) showed higher SCBD values, whereas r‐like taxa (rotifers and small cladocerans) were more frequent in the most phosphorus‐enriched, high‐LCBD sites. Community composition differed between habitats and ecosystem types, but not between seasons; it was dominated by species turnover and showed high among‐cave dissimilarities without clear distance–decay. Our findings indicate that subterranean zooplankton metacommunities in the Caatinga drylands are structured primarily by environmental filters (notably nutrient enrichment), habitat type and life‐history strategies rather than spatial distance or seasonality. Subterranean waters act as unique refuges that contribute disproportionately to regional biodiversity and should be considered in the conservation of groundwater‐dependent ecosystems in semi‐arid karst landscapes.
Puppin-Gonçalves et al. (Wed,) studied this question.