Spillway water falling from hydroelectric power plant dams in the upper Yangtze River creates a high pressure in plunge pools below the dams allowing gasses to be dissolved at high rates. The resulting supersaturation persists many miles downstream the dam which may elicit mortality in river fishes associated with gas bubble disease (GBD). We have in a two-year study (2014–15) evaluated the effect of water depth on development of GBD in an endemic and endangered fish species, the Chinese sucker Myxocyprinus asiaticus, 24 km downstream of Xiangjaiba dam. Mortality and incidence of GBD were recorded and it was seen that water depth and survival time/GBD development was positively correlated. The physiological mechanisms explaining increased resistance to GBD with increased water depths (and thereby higher hydrostatic pressure) are discussed. The results may be applied in future management of fish resources in order to protect endangered endemic fishes in rivers affected by dam constructions.