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Simple Summary Total dissolved gas (TDG) supersaturation severely threatens the survival of fish downstream of a dam in the Yangtze River due to flood discharge. However, most studies have been executed in the laboratory. Few works have evaluated the effects of TDG supersaturation on fish in natural rivers during periods of flood discharge. In the present study, we investigated the survival of two rare species (Procypris rabaudi and Myxocyprinus asiaticus) when subjected to TDG-supersaturated water at varied water depths in the natural river during periods of flood discharge. The results of this study showed that deeper water depths can increase the tolerance of juvenile Procypris rabaudi to TDG supersaturation in natural rivers during periods of flood discharge while it cannot improve the survival of juvenile Myxocyprinus asiaticus. Juvenile Procypris rabaudi were more vulnerable to TDG supersaturation than juvenile Myxocyprinus asiaticus. The study results can promote the protection of juvenile Procypris rabaudi and juvenile Myxocyprinus asiaticus (or other rare species) and contribute to the improvement of reservoir operation practices in the Yangtze River. Abstract Total dissolved gas (TDG) supersaturation, which can be caused by flood discharge, results in gas bubble disease (GBD) in fish and threatens their survival downstream of dams. TDG supersaturation has become a serious environmental problem in the Yangtze River. Few studies have evaluated the effect of TDG supersaturation on fish in natural rivers during periods of flood discharge. To estimate fish tolerance to TDG supersaturation under natural conditions, juvenile Myxocyprinus asiaticus and juvenile Procypris rabaudi were exposed to TDG-supersaturated water for 96 h at various depths (0–0.3 m, 0.3–1.3 m, 1.3–2.3 m and 0–2.3 m) during periods of flood discharge of Dagangshan hydropower station. The results showed that juvenile Procypris rabaudi and juvenile Myxocyprinus asiaticus exhibited obvious GBD signs. An increase in exposure time decreased survival probability of the two species. Deeper water depths can increase the tolerance of juvenile Procypris rabaudi to TDG supersaturation in natural rivers during periods of flood discharge while it cannot improve the survival of juvenile Myxocyprinus asiaticus. Compared with juvenile Myxocyprinus asiaticus, juvenile Procypris rabaudi showed weaker tolerance of TDG supersaturation in shallow water, and juvenile Procypris rabaudi were more vulnerable to TDG supersaturation than juvenile Myxocyprinus asiaticus even if the TDG level (116%) was low.