Nested systems of biodiversity classification are commonly used for designating protected area networks in terrestrial and marine realms. Whilst terrestrial-style protected areas are largely inappropriate for freshwater systems, the concepts of 'representative' biodiversity and 'complementarity' can be borrowed for freshwater conservation. Cryptic species are commonly found in freshwater macroinvertebrates and fish, and most have restricted distributions relative to the described conglomerate 'species'. This indicates that 'representative' and therefore 'complementary' units of freshwater biodiversity may be smaller than previously appreciated. Using recently detected cryptic species in atyid shrimps from eastern Australia (Atyidae: Paratya australiensis, Caridina mccullochi and C. indistinca), we tested predictions about regional patterns of cryptic assemblage structure, endemism and Phylogenetic Diversity (PD) at the river scale, and discussed their implications for freshwater conservation. Patterns of distribution in these cryptic shrimp species largely corresponded with published distributional patterns of cryptic species in several freshwater fish in eastern Australia, and indicated the presence of four putative ecoregions within a previously recognised freshwater fish province (Eastern Province). However, some rivers had pronounced cryptic endemism, suggesting that rivers may not be 'representative' of one another's biodiversity even within ecoregions. PD and endemism were largely correlated with one another, as endemics typically co-occurred with widespread species at the river scale. This study indicates that cryptic species can contribute to defining patterns of biodiversity at nested spatial scales that may be important for freshwater conservation.