Abstract <p>The Volga River Delta, as one of the largest deltas in the world, has a wide variety of hydrological features, which creates a wide range of conditions for the development of diatoms. The aim of this work is to study the species composition of diatom assemblages of the surface layer of bottom sediments in modern watercourses of the delta of the Volga River and to identify the characteristics of the distribution of species depending on the habitat and the main indicator species of these habitats. This work will serve as a basis for the creation of a diatom database and its further application in paleoecological reconstructions. The diatom analysis method was used to study 24 samples of the surface layer of bottom sediments collected using a bottom grab from water bodies of various hydrological characteristics on the territory of the Damchik section of the Astrakhan Biosphere Reserve. The most common species in the studied objects are: <i>Aulacoseira granulata</i>, <i>Aulacoseira ambigua</i>, <i>Stephanodiscus minutulus</i>, typical for the phytoplankton of the Volga River. One object, the Gryaznukha channel, is distinguished by the composition of dominant species—<i>Cocconeis placentula</i>, <i>Cocconeis pediculus</i>—and a high proportion of the benthos (77–99%). Analysis of samples collected in watercourses along the profiles showed a difference in the ratio of plankton and the benthos depending on the depth: in deeper areas, an increase in the proportion of planktonic species was found. The results of diatom analysis were also studied using the principal component method. The most significant factor in the formation of diatom complexes in the studied samples is the depth of the watercourses. The principal component method reliably identifies a cluster of samples from the deepest sections of the Bystraya River and one sample from Sazanii Bay, collected near the Bystraya River, as the characteristic species <i>Aulacoseira ambigua</i> and <i>Stephanodiscus minutulus</i>.</p>