The Caspian Sea has undergone tremendous changes due mainly to anthropogenic influences. From the 2013 record (January and April), studies were done in the southwestern Caspian Sea (off Jefrud), to gauge the impacts of fish cage culture on the zooplankton community. Scientists found a total of 12 species of zooplankton, belonging to 9 taxa at the study sites. As compared to the 1996–1997 records that marked a total of seven Copepode species at the same study area, only one species was recorded in 2013. The same applied to Cladocera, with only Pleopis polyphemoides documented in 2013. Acartia tonsa and Balanus improvisus were the most dominant species found at most sites, whereas Bivalvia larvae of Pleopis polyphemoides and Synchaeta sp. were noted only in January of 2013. Zooplankton abundance varied greatly between 1600 and 14,500 ind.m−3, dependent on site and period of study. Further check with PCA method confirmed the spatial variations between fish cage culture sites and the references sites. Conclusion is drawn to rectify the impacts of fish cage culture on zooplankton population structure, based on the significant abundance of A. tonsa, B. improvisus, P. polyphemoides, and Bivalvia larvae at the fish cage site as compared to the reference site.