The impact of atmospheric deposition on seas and oceans requires consideration of interfacial processes within the sea surface microlayer (SML), the uppermost layer at the air-sea interface. This study examines the impact of anthropogenic (AA) and biomass burning (BB) aerosol particles on plankton community structure and organic matter accumulation in the SML compared to the underlying water (ULW; 1 m depth) through microcosm amendment experiments in the coastal Adriatic Sea. Results confirm that realistic additions of AA and BB aerosols affect the SML and ULW differently, highlighting complex interactions between nutrient availability, toxicity, and plankton species competition. The sudden supply of nutrients, like nitrogen favoured larger phytoplankton, while elevated trace metals and organic pollutants could have a toxic effect, particularly on smaller species. The study highlights the vulnerability of the neuston community in the SML to pollutants, as the higher UV radiation likely enhanced the toxicity of specific atmospheric components compared to the ULW plankton community. Changes in neuston diversity due to atmospheric deposition strengthened the SML accumulation of dissolved and particulate organic carbon, including surfactants, which may reduce CO2 exchange between the ocean and the atmosphere. This study is one of the few to highlight the critical role of the SML in understanding the broader impacts of atmospheric deposition on marine systems, advancing our knowledge of environmental interfaces and their role in mediating increasing environmental pressures. The dataset of the microcosm experiment is archived, and on the first sheet, there is an explanation of the abbreviations used in the document