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. 1. Nowadays, it is widely accepted that increasing human activity is highly related to the current biodiversity loss, this fact being especially worrying in aquatic ecosystems, mainly in semi-arid areas. To date, studies on the biodiversity of small standing waters are focused on Central and Northern Europe, Mediterranean regions being poorly documented. 2. Here, data for aquatic Coleoptera in SE Iberia have been used to: (i) explore the relative contribution of standing waters to regional aquatic biodiversity, (ii) identify the environmental drivers structuring beetle assemblages, (iii) determine the degree to which standing water assemblages are nested subsets, and (iv) make recommendations for the conservation and management of the habitats studied. 3. Water beetles are a hyperdiverse group of aquatic insects which represent good surrogates of aquatic biodiversity. A total of 95 sites across eight habitat types were sampled, 174 species being recorded (11% were Iberian endemics). 4. Habitat types generally had distinct aquatic beetle faunas; a combination of conductivity, anthropogenic impact and altitude best explaining differences in assemblages across sites. Beetle faunas were significantly nested, this being the case across all sites, and for both fresh and saline systems independently. Disturbance was identified as a key driver of nestedness across sites overall, and particularly in freshwaters, whereas conductivity was more important in saline waters. 5. Our study identifies the biodiversity importance of lentic inland waters in the Iberian southeast, and points to the influence that human activities already exert on the invertebrate faunas of western Mediterranean wetlands.