We studied the communities of the invasive Balanus improvisus and native Cerastoderma glaucum populations in the south-western Caspian Sea. The massive movement of live Bivalvia attached to Cirripedia colonies along the studied coastline strengthens the hypotheses asserting the possible negative effects of exotic species on endemic species. Different live stages of both animals including meroplankton and macro-invertebrates were considered in the analysis. Bivalvia larvae showed a downward trend in population, in contrast with an upward trend of Cirripedia larvae from 1996 to 2013. The abundance of C. glaucum decreased west to east along the sea shore in contrast with increasing biomass of B. improvisus. Both Bivalvia and Cirripedia larvae did not show any overlapping temporal abundance. The Cirripedia larvae showed its highest abundance in winter while the bloom of Bivalvia larvae occurred in April and May during 2004–2013. The biomass of B. improvisus reported in this study was higher than those reported for the northern parts and for the middle parts. Distribution patterns of both species were described based on temperature, salinity gradient and local nutrient content. A non-linear growth model of Bivalvia showed the short-term effects of Cirripedia on Bivalvia growth. The controversy between the effects of Cirripedia on the movement of two different Cardiidae (C. glaucum, which is affected by the presence of B. improvisus, and Adacna vitrea with no attached Cirripedia) highlights the contributing role of several other factors including ecosystem degradation.