The distributions of freshwater fauna in the La Plata Basin, including decapods, are dynamic; their actual distributions depend on not only their movements but also on environmental fluctuations. The La Plata system has a diverse range of environments, which are colonized by crustaceans with complex evolutionary histories. Our aim was to elucidate the distribution patterns and relationships of current freshwater decapod fauna in terms of the different geo-climatic processes at work in the La Plata system. We recognized 13 zones based on their unique environmental characteristics. Species lists were assembled through field samples, examination of museum collections, and literature analysis. Faunistic similarity was evaluated using the Jaccard index and cluster analysis. A parsimony analysis of endemicity (PAE) was applied to determine the most parsimonious of all possible tree topologies. There were 69 species freshwater decapods analyzed in the La Plata Basin. The Mata Atlántica (MA), Paraná Superior (PS), and Uruguay Superior (US) zones are distinguished by their high species richness values, whereas the western and southern basin regions exhibit the lowest species richness values. The Paraguay-Pantanal (PP) and Paraguay-Pilcomayo-Bermejo (PPB) zones share some prawn taxa with the Amazon Basin. The eastern zones of the La Plata Basin were grouped by the presence of several species of the genera Parastacus, Aegla, and Trichodactylus. The northern, central, and western zones were characterized by species of the genera Dilocarcinus, Sylviocarcinus, and Zilchiopsis. According to the PAE analysis, two major zones were recognized in relation to the presence of freshwater decapods (eastern and western-central zones). In the western-central zones, three sub-areas were identified; one shares species with the Amazon basin the others have a relationship with the eastern and northern regions and represents a region that is strongly influenced by a temperate climate and therefore possesses diminished species richness values.