Benthic assemblages of the Small Aral Sea were studied in 1999. The species composition, density, and biomass of benthic invertebrates were determined. The vertical distribution pattern and its dynamics in the course of desiccation of the sea were analyzed. It is shown that the vertical distribution of the benthos has changed substantially over the last 30 years. The biomass of the benthos in the inshore zone increased, while in the central part of the sea, benthic invertebrate populations declined and gradually disappeared. These changes are likely to be due to the accumulation of organic matter in the bottom sediments and the weakening of hydrodynamic processes, which could lead to oxygen depletion in deep water. In the 1990s, the benthic assemblages of the Small Aral Sea were relatively stable and highly productive. It is concluded that the Aral Sea is a promising area for fishery restoration.