Shallow brackish water habitats are characterized by highly unstable environmental conditions, which result in low species diversity. We performed our research in the Vistula Lagoon in three seasons in the years 2019–2021. This lagoon is characterized by extremely variable environmental conditions, and our research covered the period of hydro-technical works before opening the canal through the Vistula Spit, which could be an additional stress factor. The aim of our study was to present the particularities of zooplankton communities (Rotifera; Crustacea) in the shallow coastal ecosystem. Our results pointed out very low diversity of zooplankton which could be caused by multi-stress conditions related to increased turbidity and low salinity. Nevertheless, under these conditions, some species achieved an advantage and strongly dominated the zooplankton communities. Domination of Eurytemora affinis in the Vistula Lagoon as well as in other brackish habitats is a well-known phenomenon. Moreover, the Vistula Lagoon offered favorable conditions for the intense development of non-indigenous, or alien, species like Diaphanosoma mongolianum, D. orghidani, and Acanthocyclops americanus. Therefore, brackish waters seem to be favorable transitional areas for non-native fauna that may subsequently spread into adjacent freshwater and marine systems.