Aquatic ecosystems have changed dramatically over the last decades. For example, by reducing the water flow in the rivers, organic material would increase in the lower zone of rivers resulted in fluctuating biodiversity of macro-benthic communities. The aim of this study was to determine the changes in macrobenthic diversity in the lower zone (or estuary) of Gharesou river - southeastern Caspian Sea, in where hatchery-reared juvenile fish like Rutilus rutilus (Linnaeus, 1758) and Sturgeon fish (Acipenser sp.) are released for stock enhancement. Sampling was undertaken over five surveys in four sites in the lower zone (or estuary) of river to study the abundance, species richness, and biodiversity indices of macrobenthos. The results of split plot analysis showed that sedimentary organic matter in river litter reduced significantly in the second survey, due to relatively heavy rain fall occurred before second sampling. Whilst, biodiversity indices had no significant differences among surveys (p>0.05), these indices showed significant differences among sampling sites. Species abundance in the third survey increased significantly (p<0.05), related in sharp increment of Tubifex abundance in the fifth site. Rising abundance of Tubifex in the fifth site resulted in significant reduction of diversity indices like Shannon index and inverse-Simpson, and also significant increment of Berger-Parker index, which was probably associated with higher resistance of this species to the hard environmental condition like reduction of water flow in the river. Whilst, diversity indices in the release site for hatchery-reared juvenile was not significantly more (diverse) than the other sites(p>0.05), and also dissolved oxygen and NO3, and NH4 in the release timing had the higher and lower rates, respectively; higher fluctuations of salinity and total dissolved solids in the release site could impact survival of released hatchery reared juvenile. Thus, it is recommended that hatchery reared juveniles being released more far from the estuary towards the upstream.