<p>Meroplankton consists of the larvae of fish and benthic organisms, and plays a crucial role in linking pelagic and benthic ecosystems. However, research on zooplankton in the Baltic Sea has usually focused on holoplankton; thus, there are still significant gaps in knowledge about meroplankton and its seasonal variability. Consequently, as one of the first Baltic studies, we focused solely on the meroplankton community and its seasonal and spatial changes. Samples were collected monthly, year-round, between May 2021 and April 2022 from four stations located in the Gulf of Gdańsk, along a transect from the shallow Vistula River estuary to the Gdańsk Deep. The analysis of meroplankton resulted in the determination of 12 types of larvae belonging to 8 classes, and indicated that bivalves and polychaetes were the dominant components of the community. Meroplankton abundance and taxonomic composition showed high seasonality, with the highest abundances in summer, and spatial gradients in taxa diversity along the sampling transect. Additionally, statistical analysis revealed a key role of temperature in structuring the community. Taking the role of meroplankton into account, we propose more research in the Baltic Sea, possibly with the use of novel methods, and a greater focus on meroplankton in monitoring programs.</p>