The freshwater fauna of nine caves in central Abkhazia, western Caucasus, revealed 35 species of stygobionts, including 15 new species to be described elsewhere. The number of species per station increased from the depth towards the entrance in caves Golova Otapa and Abrskila, becoming the highest in the epigean part. In both caves, two abundance peaks of aquatic invertebrates were registered: one in the entrance area, associated with the development of amphibiotic insect larvae, the other in the depths due to the high numbers of stygobionts. In Cave New Athos, the highest species richness and abundance were observed in large lakes. In caves Golova Otapa and Abrskila, two faunistic complexes with complementary distributions were found, the first due to amphibiotic insects in the cave entrance area, the second one composed of stygobionts in the deep areas. The impact of anthropogenic factors on aquatic cave communities was also noted. The stygobiotic faunas of all caves studied were clearly divided into three groups, following the number of river valleys in which they were situated. The stygobiont faunas of the caves located within one river valley appeared to be 50% similar. In contrast, the fauna composition of the stygobionts from caves situated in different valleys shared not more than 12% species in common. Stygobiotic shrimps and gastropod mollusks show profound local endemism. Stygobiotic Amphipoda penetrating the ground waters revealed wide distributions between cave systems within a single karst massif.