Atmospheric deposition is the dominant pathway for the loading of exogenous nitrogen (N) to open ocean. Here, rainwater samples were collected from 31 stations in the equatorial East Indian Ocean (EIO) and West Pacific Ocean (WPO) to explore the spatial variability of N species, potential sources, and related ecological influences. Among two oceans, nitrate (NO3–) and ammonium (NH4+) were the main components in the rainwater N inventory. NO3– concentrations varied from 0.19 to 100.5 μM, whereas NH4+ concentrations ranged from 0.54 to 110.6 μM. Among all stations, low concentrations of NO3– and NH4+ appeared in the remote ocean, whereas high concentrations were observed at the stations near the Malacca Strait and New Guinea, coupled with an enhancement of non-sea salt major ions, e.g., calcium ions (Ca2+) and sulfate (SO42–), revealing the influence from coastal human activities, such as coal and gasoline combustion. In the remote ocean, δ15N–NH4+ ranged from −5.7 to −9.3‰, whereas it dropped to -15.5‰ near coasts. A logarithmic decay between δ15N–NH4+ and NH4+ concentrations in rainwater samples was obtained, suggesting a shift from natural source (seawater emission) in oceanic precipitation events to anthropogenic source (chemical fertilizer volatilization and vehicle exhaust) in coastal rainwaters. δ15N–NO3– in the remote ocean varied between −1.7 and 0.4‰ with low levels found in the WPO, likely related to the ascending air flow driven by the Walker Circulation. In coastal oceans, δ15N–NO3– ranged from 1.5 to 3.5‰. The linkage between δ15N–NO3– and NO3– concentrations varied in two oceans, resulting from difference in biological and fossil fuel combustion contributions. Compared with ocean surface water, N in the rainwater was markedly enriched, suggesting that N from atmospheric wet depositions could rapidly enhance the dissolved N availability in ocean surface water. However, the N redundancy according to the Redfield–Brzezinski ratio (N:Si:P = 16:16:1) in the rainwater might benefit from the growth of N-preference phytoplankton species and microbes. As the first study on N concentrations, sources, and stoichiometry balance in rainwater over the equatorial WPO and EIO, the results could be a support to the global N budget estimation and oceanic primary production modeling.