In June 2015, aboard the r/v Akademik Ioffe, a study was conducted on the surface zooplankton community in selected Baltic Sea basins along the Arkona Basin - Gulf of Gdansk route. Samples were collected using a 100 μm mesh plankton net at depths of 2–0 m. Additionally, optical and physical properties were assessed through remote (lidar) and in-situ (CTD and surface microlayer seawater sampling) measurements to provide a foundation for biological analysis.The zooplankton included 19 taxa from holoplanktonic Copepoda, Diplostraca, Rotifera, and meroplanktonic stages of Bivalvia, Gastropoda, Polychaeta, Cirripedia, and Pisces. Zooplankton abundance ranged from 37399 ind. m−3 (Slupsk Furrow) to 267744 ind. m−3 (Bornholm Basin), with copepods being the most numerous groups. While the zooplankton community composition was relatively stable across the study area, their distribution varied. The most diverse station was Slupsk Furrow, with Copepoda, Diplostraca, Rotifera, and meroplankton making up approximately 40%, 25%, 20%, and 5%, respectively. In contrast, Bornholm Basin had the highest zooplankton numbers, mainly dominated by copepods (90%) with minor contributions from other groups.Fluorescence properties of surface microlayer organic matter were assessed by measuring the intensity ratio of the primary fluorophores (A, C, M, and T) of dissolved organic matter molecules, represented as (M + T)/(A + C). This indicated a mixed marine-terrestrial nature of organic matter in stations west of the Slupsk Furrow. Stations at the Arkona Basin and the Slupsk Furrow had the highest ratio values, suggesting a significant marine organic matter source. In contrast, stations east of the Slupsk Furrow exhibited lower (M + T)/(A + C) ratios, indicating a dominant terrestrial origin for organic matter. Lidar results further supported the division of the study area into two regions based on bio-optical properties: a western region (Arkona Basin, Bornholm Basin, and Slupsk Furrow) and an eastern region (Gotland Basin and Gdansk Basin). Moreover, the variability in zooplankton community structure and distribution is closely correlated with the water hydrographic and optical characteristics. We can therefore conclude that all the water properties that we have studied are a derivative of the interaction of sea and land.
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