The taxonomic composition and dynamics of the abundance of holoplankton and meroplankton were studied in the estuary of the seaport Temryuk and in Temryuk Bay (background) in autumn 2018. The impact of the trading port and the Kuban River on the state of holoplankton and meroplankton was assessed. The abundance of holo- and meroplankton in the more desalinated and polluted estuary of the port, which borders the Kuban River, was 1.5–3 times lower than in the Temryuk Bay. In the composition of the copepods Oithona davisae and Acartia tonsa, up to half of non-viable individuals were found in the port estuary. In early autumn, the holoplankton was dominated by Oithona davisa and freshwater cyclopoid copepods; in Temryuk Bay, O. davisae prevailed; in meroplankton, larvae of mollusks wee ubiquitous. At the end of autumn, freshwater cyclopoid copepods and larvae of cirripede barnacles Amphibalanus improvisus were abundant in the port estuary; in the bay, along with O. davisae, brackish-water copepods Еurytemora affinnis, larvae of cirripede barnacles A.improvisus were abundant. The basis of the pool of merorplankton was species tolerant to water eutrophication and sulfide contamination of bottom sediments (A. improvisus, Bittium reticulatum and Bivalvia).