The distribution of four morphologically similar and narrowly endemic Niphargus species living mainly in surface waters of the western Dinaric region was studied. The study area consists of limestone and marls-sandstone (flysch) patches. The variable chemical structure of the flysch affects water conductivity and carbonatic hardness. N. timavi inhabits surface and subterranean waters of low conductivity and carbonatic hardness, both on limestone and flysch. N. spinulifemur is restricted to surface waters with high conductivity and higher carbonatic hardness, exclusively on flysch areas. N. vinodolensis sp. n., described herein, lives both on karst and flysch, where waters exhibit intermediate values of conductivity and carbonatic hardness. N. krameri inhabits surface and subterranean waters with high conductivity and high carbonatic hardness, both on limestone and flysch. This species is in the course of morphological differentiation with three morphological races, probably due to low dispersal ability. The studied species probably do not constitute a monophylum. The easternmost species, N. vinodolensis shows (morphologically, molecularly) close relations with the northeast-Italian N. elegans and with middle-Dalmatian N. illidzensis dalmatinus. It is possible that they differentiated from a common ancestor which inhabited the dry bottom of the northern Adriatic, exposed during the last glacial. We assume that the reasons for the high degree of endemism are historical changes of hydrographical regimes and sea transgressions–regressions. Poor migratory abilities in a geologically diverse landscape restricted further dispersal.