Total dissolved gas (TDG) supersaturation caused by the operation of hydropower stations can threaten the survival and swimming performance of fish species. Different modes of hydropower flood discharges (regular vs. intermittent) from the Dagangshan hydropower station in China were studied in July and September 2017 to study the impact of TDG supersaturation on two native fish species in the downstream Dadu River. The average TDG supersaturation value was 114.3% in July under the regular discharge mode. In September, the supersaturation of TDG fluctuated in response to the intermittent discharge mode with an average TDG of 119.3%. Apparent gas bubble trauma was found on young-of-the-year (YOY) Prenant's schizothoracin and elongate loach in cages at different water depths during the flood discharge period. The mortality rate of YOY Prenant's schizothoracin and elongate loach in cages with water depths of 0–1 m were 16.25% and 2.5%, respectively, in July. The fluctuating TDG levels with higher peaks in September caused higher fish mortality rates. The final mortality rates of YOY Prenant's schizothoracin and elongate loach in cages with water depths of 0–1 m were 75% and 33.75%, respectively. Fish in the cages at a 0–3 m water depth survived better than those in the cages at a 0–1 m water depth. The critical swimming speeds (U_crit) of YOY Prenant's schizothoracin and elongate loach without exposure to TDG supersaturation were 11.64 and 16.76 BL s⁻¹, respectively. U_crit decreased significantly after experiencing the flood discharge period and recovered to the normal level after experiencing the corresponding interval period.