In the present study, changes in benthic communities due to seasonal changes in the water of the southern Caspian Basin were investigated. Sampling was conducted monthly, from March 2006 to March 2007, at six selected stations in Tajan River mouth located on south eastern Caspian Sea. Also secondary benthic production consumable for fish and other biota inhabiting the mouth and adjacent areas were estimated. Forcing and limiting factors were also discussed. Benthic communities comprised 9 taxa, of which Ballanus sp., Chironomus plumosus and Cerastoderma lamarki were the main contributors to both overall biomass and secondary production. Annual secondary production varied from 3.8g AFDWm-2 y-1, in the upper part of the mouth, to 78.06g AFDWm-2 y-1 in the center of the estuary area. Multivariate correlations between environmental variables and the macro benthic biomass highlighted the role of the water level, temperature, organic carbon content and dissolved oxygen which resulted in separation of communities in the estuary. Composition, biomass and secondary annual production of macro benthic communities were dramatically affected by changes in water residence time and summer drought crises. The isolation of this habitat limits the recovery of other benthic fauna during drought periods. Only populations of two taxa, Balanus sp. (Cirripeda) and C. plumosus (Diptera) seemed to be able to recover quickly after the drought crises, which, in turn, could compromise the overall secondary production, which may have negative effects on fish and other superior organism’s survival. During summer water renewal, when agricultural activities are intense, nutrient inputs should be regulated in this estuary to reduce the risk of benthic mass mortality and to ensure a sustainable ecosystem.