Riverine fishes have been increasingly threatened by the global proliferation of both small dams and large hydropower projects to meet the soaring water, energy and food demands from growing human populations and urbanisation. However, empirical evidence of the direct effects on a specific species before and after dam construction and operation is rare. Causes of population decline vary among species and, although little known, they are of great importance for successful environmental flow regulation. We monitored the hydroenvironment and population dynamics of a Schizothoracinae fish (Schizothorax lissolabiatus) for 9 years before and after dam (i.e., Dahuaqiao) construction in the upper Mekong River to understand fish response processes and the underlying mechanisms. Optimal hydroenvironmental conditions for key reproduction stages (e.g., pre-spawning, hatching and post-hatching) were reconstructed using daily increment analysis of larval otoliths and hydroenvironmental data. The flow regime was substantially disrupted by the dam, and water temperature was only slightly changed. The disappearance of young of the year from downstream after dam operation indicates that the changed hydroenvironment caused recruitment failure in S. lissolabiatus. By matching optimal hydroenvironmental conditions for S. lissolabiatus reproduction with the monitored hydroenvironmental data series before and after dam operation, we found that changes in thermal regime alone caused narrowing of the reproduction window by an average of 41%, whereas flow-regime change alone narrowed it by 96% and it was narrowed by 98% for thermal and flow changes combined. This study shows that the altered flow regime, but not the thermal regime, was the primary driver of the recruitment failure of S. lissolabiatus. The findings highlight the importance of prioritising flow-regime management to improve recruitment success for S. lissolabiatus and to favour the persistence of other imperilled Schizothoracinae fishes and native species in dammed rivers.