During the global nuclear weapon tests, large amounts of radioactive elements are released into the environment. Long-period actinide elements such as Np, Pu, and Am exhibit different behaviors in various environments, and their isotope characteristic fingerprints are of great significance for studying the distribution, migration, and prediction of radioactive pollutants. To investigate the distribution of 241 Am and 237 Np in southern China, activities of 241 Am (0.008 ± 0.012−0.932 ± 0.066 Bq/kg) and 237 Np (0.037 ± 0.003−1.458 ± 0.063 mBq/kg), 237 Np/ 239 Pu atom ratios (0.055 ± 0.003−0.864 ± 0.054), and 241 Am/ 239+240 Pu activity ratios (0.033 ± 0.075−15.870 ± 0.477) in 95 surface sediment samples collected from the northern South China Sea and major river basins were analyzed for the first time. Due to the different scavenging mechanisms of Am and Pu, 241 Am is preferentially concentrated by sinking the particulate, while plutonium is scavenged in the coastal area, resulting in a higher 241 Am/ 239+240 Pu activity ratio in estuary and coastal areas. The distribution of 237 Np shows obvious spatial inhomogeneity as the high migration rate. The relevant fingerprint characteristic has changed greatly and needs to be updated urgently. As a result of the convergence of land and sea, 241 Am, 239,240 Pu, and 237 Np are dominated by terrestrial sediments and deposited in the coastal area of southern China, which should be paid more attention to. This work can establish China's current neptunium radioactivity database, and the difference in Np, Pu, and Am scavenging processes may be a powerful tool for evaluating the impact of the Pearl River Estuary salt tide.