Coastal zones are extremely vulnerable and, at the same time, anthropogenically pressed. Excessive enrichment of marine waters with nutrients and organic matter can lead to “red tides”, oxygen deficits, decreasing assimilation capacity, etc. The purpose of this work is to study atmospheric precipitations as a source of nutrients directly affecting waters of the coastal areas of Crimea and, ultimately, strengthening eutrophication consequences. In 2004–2008, and from 2015 to present, samples of atmospheric precipitations have been collected at the Marine Hydrometeorological Station in Sevastopol. They have been analyzed for the content of inorganic nitrogen, phosphorus, and silica. For 2009–2014, direct measurements are unavailable and a previously retrieved multiple nonlinear regression equation has been used to estimate the concentration of inorganic nitrogen in atmospheric precipitations depending on meteorological conditions, including the number of precipitations, number of days without precipitations, relative air humidity, wind direction vectors, and air temperature. Data obtained in this study have revealed that atmospheric precipitations are one of important inputs of nutrients for local areas. Their relative contribution increases on the time scale of days, while the role of rivers remains the most important on the annual scale. The contribution of atmospheric precipitations to the inventory of nutrients becomes more significant in the summer, when seasonal stratification in the water column prevents vertical mixing of waters, and the ambient concentration of nutrients in the upper layer of water is minimal.