This paper focuses on the atmospheric dust transport effect on the changes in chlorophyll-A concentration in the Black Sea surface layer. In order to assess the input of nutrients with atmospheric precipitations at the Crimean coast of the Black Sea, the collected samples were analyzed for the content of inorganic nitrogen, phosphates, and silicon. The samples were taken into a wet-only sampler and into a permanently open one, to assess the effect of dust on the nutrients concentration in dry depositions. Cases of multi-fold excess of the nutrients content in the open sampler collected precipitation over that in the wet-only sampler were identified. For such high concentration cases, the 7-day back-trajectories analyses was carried out using the model of the international network AERONET and the HYSPLIT model. The results of our research showed that the influx of nutrients with the atmospheric depositions can result in increasing of chlorophyll-A concentration in 11–36% in the surface layer of the Black Sea. After atmospheric depositions, concentration of phosphates in the surface layer can increase more than five times compared with the background concentration. The increase of silicon concentration can reach 30%. The influx of atmospheric precipitation containing significant amounts of nutrients into the bay can shifts the Redfield ratio compared with background value up to three times.