A new data set of seasonal stable water isotopes (δD and δ¹⁸O) and temperature-salinity profiles was applied to improve our understanding of water mass distributions and their impact on the environment of the Beibu Gulf (BG). Our study revealed that the coastal current (CC), West-Guangdong coastal current (WGCC), and South China Sea water (SCSW) were the three dominant water masses in the BG, and their influence was exhibited in seasonal variations. The CC was the dominant contributor to the BG water during summer (43%) and fall (45%), while it changed to the intrusion of SCSW with higher salinity in winter (57%). The contribution of WGCC to the BG was relatively stable during the three seasons (24%–31%). In addition, the nutrients in the BG were greatly affected by different water mixing occurring in the gulf. The nutrients mainly originated from the CC in summer (52%–68%) and fall (32%–69%), while the dominant source shifted to the WGCC in winter (36%–69%). Moreover, the contribution of SCSW to the nutrients loading (15%–49%) in the BG was relatively high due to its high contribution (57%) to the BG water during winter. These indicated that the BG has a stable input of external nutrients from different water masses to sustain primary production in the BG. Our study uses dual water isotopes to quantify the seasonal intrusion of water masses and their impact on nutrients, providing a new method to study the impact of the distribution of water masses on nutrients in the gulf.