Abstract: The aim of this study was to reveal the causes of death in aquatic leaves by analyzing leaf anatomy and photoinhibition of photosystem II (PSII) in Oenanthe javanica seedlings. Total biomass, leaf relative water content (RWC), chlorophyll a fluorescence transience and leaf anatomy were measured during total submergence. Submergence resulted in a significant reduction in total biomass and Fv/Fm ratio in terrestrial leaves. However, the maximal quantum yield of PSII photochemistry (Fv/Fm) and electron transport did not differ between normal terrestrial leaves and aquatic leaves. In vivo, the RWC and Fv/Fm ratio did not decrease significantly after plants were exposed to weak light; Never the less, under moderate and high light conditions, the RWC and Fv/Fm ratio significantly decreased after 2 h treatment. In in vitro experiments, Fv/Fm ratio in aquatic leaves were not significantly affected by moderate light, and it was restored to its initial value under weak light; however, the Fv/Fm ratio decreased significantly under high light and failed to recover completely under weak light. Structurally, as compared with terrestrial leaves, aquatic leaves had lower total thickness, upper epidermis layer, lower epidermis layer and stomatal size; however, the palisade parenchyma and spongy parenchyma of aquatic leaves did not differ. The stomatal density of the upper epidermis was higher than that of terrestrial leaves. The performance of PSII in terrestrial leaves declined quickly with total submergence, but submergence had no obvious effects on newly developed leaves. When the plant was re-exposed to a terrestrial environment, the changes in the structure of aquatic leaves caused a large decrease in its water-retention capacity under light, whereas high light led to pronounced photoinhibition and inactivation of PSII. The combination of weak water-retention capacity and strong photoinhibition accelerated the damage of the photosynthetic apparatus in the field, which resulted in the death of the aquatic leaves.