In low-nutrient low-chlorophyll areas, such as the Mediterranean Sea, atmospheric fluxes represent a considerable external source of nutrients likely supporting primary production, especially during periods of stratification. These areas are expected to expand in the future due to lower nutrient supply from sub-surface waters caused by climate-driven enhanced stratification, likely further increasing the role of atmospheric deposition as a source of new nutrients to surface waters. Whether plankton communities will react differently to dust deposition in a warmer and acidified environment remains; however, an open question. The potential impact of dust deposition both in present and future climate conditions was investigated in three perturbation experiments in the open Mediterranean Sea. Climate reactors (300 L) were filled with surface water collected in the Tyrrhenian Sea, Ionian Sea and in the Algerian basin during a cruise conducted in the frame of the PEACETIME project in May–June 2017. The experiments comprised two unmodified control tanks, two tanks enriched with a Saharan dust analogue and two tanks enriched with the dust analogue and maintained under warmer (+3 ∘C) and acidified (−0.3 pH unit) conditions. Samples for the analysis of an extensive number of biogeochemical parameters and processes were taken over the duration (3–4 d) of the experiments. Dust addition led to a rapid release of nitrate and phosphate, however, nitrate inputs were much higher than phosphate. Our results showed that the impacts of Saharan dust deposition in three different basins of the open northwestern Mediterranean Sea are at least as strong as those observed previously, all performed in coastal waters. The effects of dust deposition on biological stocks were different for the three investigated stations and could not be attributed to differences in their degree of oligotrophy but rather to the initial metabolic state of the community. Ocean acidification and warming did not drastically modify the composition of the autotrophic assemblage, with all groups positively impacted by warming and acidification. Although autotrophic biomass was more positively impacted than heterotrophic biomass under future environmental conditions, a stronger impact of warming and acidification on mineralization processes suggests a decreased capacity of Mediterranean surface plankton communities to sequester atmospheric CO2 following the deposition of atmospheric particles.