In a survey for conservation of non-marine aquatic systems, the ostracod compositions of 43 water bodies sampled in central Spain were analysed by multivariate ordination (DCA) and classification (TWINSPAN) methods, showing a clear division in lake typology. The wide variety of life modes and habitat requirements of non-marine ostracod species yields assemblages of species of value as ecological indicators. Endorheic shallow lakes, highly temporary, are characterized by an assemblage of circum-Mediterranean and endemic species. Karstic and more stable lakes are inhabited by northern Holarctic or Palaearctic species, depending on the history and environmental conditions of the water body. Between these two extremes, the study of ostracod assemblages permits the distinction, on a finer scale, of a gradient of lake types with different disturbance conditions, resulting from a combination of hydrological, climatic, chemical and anthropogenic factors. At the extreme of that gradient, highly tolerant cosmopolitan species play an important role in the ostracod community of sites severely affected by human activities.