To infer their habitat preferences and downstream migration, spatial and temporal distributions of larvae and juveniles of the migratory riverine spawning Labeobarbus species were studied from December 2009 to November 2010 in the Gumara and Gelda Rivers, tributaries of Lake Tana. Larvae and age 0+ juveniles were collected using D-frame and seine nets. Physico-chemical variables were also assessed. Based on qualitative observations of the flow gradients as well as principal component and cluster analyses of physico-chemical variables, the seventeen sampling sites were categorized into five major habitat types: downstream pools, upstream pools, margin pools, steady flow and riffles. Larvae were present only in the highly oxygenated riffle habitats. The highest mean monthly abundance of 0+ juveniles was found in the margin pools (627 juveniles/100 m2; P < 0.05), followed by upstream pool habitats (117 juveniles/100 m2). The lowest monthly abundance was found in the downstream pool habitats located near the lake (12 juveniles/100 m2). Age 0+ juveniles were rare in the steady flow habitats and missing in the riffles. In the relatively pristine river, Gelda, juveniles move into the downstream pools when upstream and margin pools became water stressed in the driest months (March-May) and enter into the lake in the onset of the rainy season (June/July). However, in the highly perturbated river, Gumara, downstream movements of 0+ juveniles were impeded due to disconnection (in April/May) of the pools, because of water pumping for irrigation. After this disconnection, the mean monthly abundance of juveniles in the upstream pools of this river sharply declined by 57%. This study showed that age 0+ juveniles of the migratory riverine spawning Labeobarbus species stay in the pools of the rivers until the rainy season. Thus, loss of these functional habitats in the rivers would accelerate extinction of the already declining endemic Labeobarbus species flock.