Aquatic macrophytes constitute essential bioindicators of the ecological status of Mediterranean wetlands. We evaluated 136 Andalusian wetlands across four biogeographical regions (Sierra Morena, Betic Ranges, Guadalquivir Valley, and Coastal Zone) by contrasting two methodological approaches. We compared a standard biological valuation index, based on hydrophyte valuation and total species richness, with a biogeographical assessment focused strictly on the originality, singularity, and integrity of hydrophyte assemblages. Results revealed a critical nonlinear decoupling between both metrics. Traditional valuation prioritized the Coastal and Guadalquivir zones, inflating the value of communities saturated by widespread taxa and masking their lower structural integrity. Conversely, the biogeographical analysis identified Sierra Morena as the reservoir of highest structural stability despite its natural species poverty. Furthermore, residual analysis exposed highly original hidden jewels systematically undervalued by standard protocols. Since richness-dependent metrics risk neglecting unique hydrophyte components, we propose a dual conservation strategy integrating irreplaceability and structural integrity. Ultimately, this framework provides actionable insights for the sustainable management of Mediterranean aquatic biodiversity, aligning conservation practices with global ecological sustainability goals. We caution that management decisions based solely on richness thresholds may inadvertently prioritize common habitats over functionally unique but species-poor refugia.