Nitrogen fixation (diazotrophy) is an important input pathway of nitrogen to surface oceans. Diazotrophy can occur in physicochemically complex waters, requiring new tools for assessing diazotroph biogeography and influence. I present a simple method for delineating habitats and pair it with a multi-scale ecosystem assessment of diazotroph impacts in the South China Sea (SCS). This strategy identified clear habitat-specific trends in diazotroph influence across the plankton food web, indicating that diazotrophy is more prevalent in the SCS than previously thought.