The southeast of the Iberian Peninsula is a recognized area of high aquatic biodiversity, water beetles being one of the most well-known groups contributing to such biodiversity. The standing waters of this area show a high habitat diversity, occurring fresh, saline, temporary, permanent, karstic, endorheic, and artificial small water bodies. Despite this, there has been no attempt to analyze their contribution to local biodiversity. In this work, we identify the species inhabiting standing waters, analyze their contribution to the checklist from the study area, and recognize the species exclusive to this kind of habitat. We also highlight the most threatened species, identify the habitats which constitute biodiversity hotspots for this group, explore patterns of water beetle assemblage composition, and identify indicator species associated with each habitat type. We collected 125 species, 55 of them being typical to lentic habitats, in the set of 26 sampled standing water bodies, which means the 57% of the 218 species recorded in the most recent checklist for the study area. A total of 10 species are Iberian endemics and four can be considered threatened, Ochthebius irenae falling in both categories. Natural ponds showed the highest species richness (91 species), while saline water bodies (endorheic lagoons and continental salt-pans) contributed the most threatened species: Nebrioporus baeticus, Ochthebius delgadoi, Ochthebius tudmirensis and Ochthebius irenae. The most representative species for continental salt-pans was Ochthebius notabilis, for endorheic lagoons Ochthebius marinus and Hygrotus pallidulus, while Hydroglyphus geminus played this part in rice fields. Our results suggest that rice fields, endorheic lagoons, and continental salt-pans have specific water beetles assemblages, which could be used in bioassessment and conservation studies. In general, standing waters are seriously threatened in this area, particularly as a result of intensive agricultural activities. Thus, taking into account these ecosystems hold a high number of species, their continued degradation is likely to result in a significant loss of biodiversity, including key populations of a number of threatened and endemic species.