Abstract Sea spray aerosols (SSA) transport bioactive substances that affect the Earth’s environmental and climate system. We investigated the enrichment of endotoxins (LPS), characterized their influence on the SSA morphologies, and evaluated the respiratory tract deposition. LPS concentrations in SSA ranged from 0.53 to 7.36 EU m−3, with enrichment factors of 3.55–30.84. Transmission electron microscopy identified sea salt‐dominated, sea salt mixed with LPS, and LPS‐dominated particles. Among these particles, LPS‐dominated particles were preferentially enriched in the submicron SSA fraction, which represented 60.5% of analyzed particles, and may have higher exposure potential due to elevated per‐particle LPS loading. Size‐resolved deposition modeling showed that the alveolar region received the largest deposition dose, with a peak of 7.41 × 107 # h−1. These results identify particle morphology and size distribution as key controls on endotoxin exposure through SSA and provide a framework for assessing the respiratory deposition of bioactive marine aerosols.