Size is commonly used as a master trait to characterize pelagic organisms as it affects a range of processes and impact marine biogeochemical cycles and services. Yet, a holistic understanding of what environmental factors shape size structure is lacking for most mesoplankton. As part of the Pelagic Size Structure database, we explore the linkages between environmental factors and global compilations of Rhizarian, colonial N2-fixer, and Crustacean size spectra measured from Underwater Vision Profilers or benchtop scanners. We found that iron, alongside temperature, plays a disproportionate role in shaping their spectral biogeography. Our results highlight the effect of dust on N2-fixers and Rhizarians while total iron, comprising organic and mineral compounds, explained most of the variance in Crustaceans size structure. Using machine learning models, we predicted their size structure at the global scale with relatively high R2of 0.93, 0.84, and 0.66. We hope our predictions can support further assessment of their role in biogeochemical processes under present and future forcings.