Precipitation is of great significance in the transport and removal of atmospheric nutrients. For the sake of the acquaintance of nutrient level, deposition flux and secular trend of marginal sea precipitation, two decades (1997–2019) atmospheric investigations were conducted at the Qianliyan island, the western Yellow Sea. Overall, the annual average wet deposition fluxes of nitrate (NO3−), ammonium (NH4+), phosphate (PO43−), silicate (SiO32−), dissolved organic nitrogen (DON) and organic phosphorus (DOP) ranged 9.17–42.80, 13.50–41.44, 0.06–1.88, 0.07–5.56, 14.20–42.14 and 0.09–0.62 mmol·m−2·a−1, respectively. The annual average concentrations of NO3− in precipitation showed a monotonic rising trend, while that of SiO32− showed a monotonic decreasing trend. From the long-term observation, it found an alleviation of acidic precipitation of the Yellow Sea under the policy controls of sulfur dioxide (SO2) and nitrogen oxide (NOx) emissions. Meanwhile, effective control of sand-dust largely reduced precipitation SiO32− concentration. Source also effected precipitation nutrients. Average concentrations of NO3−, NH4+ and SiO32− in precipitation from the ocean were lower than those from the northern arid area, while average concentrations of PO43−, DON and DOP in precipitation from the ocean were higher than those from the northern arid area. Qianliyan precipitation brought rich dissolved inorganic nitrogen (DIN) over PO43− to the ocean surface, which might alter the phytoplankton community succession ultimately.