The construction and use of navigation and irrigation canals are among the common human alterations in landscapes and ecosystems. The North Crimean Canal (NCC) is the longest in Europe; its main branch is 403 km, and the total of all its branches exceeds 10,000 km. It is a main driver of the significant environmental changes in an all-arid part of Crimea. No zooplankton studies in the canal have been carried out up to this time at all. In 2022, zooplankton was studied in different sites from May to October. Total zooplankton abundance fluctuated between 170 and 19,560 ind. m−3, and wet biomass between 0.75 and 1057 mg m−3. In total, 11 Rotifera species, 11 Cladocera species, and 15 Copepoda species, including 2 Harpacticoida, 5 Calanoida, and 8 Cyclopoida, were found in plankton. The most common Rotifera species were Brachionus calyciflorus, Euchlanis dilatate, and Keratella cochlearis. Among Cladocera, Chydorus sphaericus, Bosmina longirostris, and Coronatella rectangular have the highest frequency of occurrence. In Copepoda, these were Acanthocyclops vernalis, Eurytemora affinis, and Nitocra typica. Among the 37 species found in NCC, 10 were not previously noted in the water bodies of Crimea. Among rotifers, they were Ploesoma hudsoni, Polyarthra dolichoptera, Pompholyx complanata, Synchaeta grandis, and Synchaeta stylata. Bosminopsis zernowi, Rhynchotalona rostrata, and Scapholeberis mucronata were not noted before among Cladocera. Eurytemora lacustris and Cyclops smirnovi were first found in Crimea among Copepoda. New technogenic aquatic ecosystems such as NCC are the “gateway” for the invasion of alien species into the new regions.