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The mean trophic position (TP) of mesozooplankton largely determines how much mass and energy is available for higher trophic levels like fish. Unfortunately, the ratio of herbivores to carnivores in mesozooplankton is difficult to identify in field samples. Here, we investigated changes in the mean TP of mesozooplankton in a highly dynamic environment encompassing four distinct habitats in the southern South China Sea: the Mekong River plume, coastal upwelling region, shelf waters, and offshore oceanic waters. We used a set of variables derived from bulk and amino acid nitrogen stable isotopes from particulate organic matter and four mesozooplankton size fractions to identify changes in the nitrogen source and TP of mesozooplankton across these habitats. We found clear indications of a shift in N sources for biological production from nitrate in near-coastal waters with shallow mixed layer depths toward an increase in diazotroph-N inputs in oceanic waters with deep mixed layer depths where diazotrophs shaped the phytoplankton community. The N source shift was accompanied by a lengthening of the food chain (increase in the TP). This may provide further support for the connection between diazotrophy and the indirect routing of N through the marine food web. Our combined bulk and amino acid δ15N approach also allowed us to estimate the trophic enrichment (TE) of mesozooplankton across the entire regional ecosystem. When put in the context of literature values, a high TE of 5.1‰ suggested a link between ecosystem heterogeneity and the less efficient transfer of mass and energy across trophic levels. [ABSTRACT FROM AUTHOR]