The effect of water temperature and flow on the migration of fish was observed using weekly inspections of a fishpass on the lowland section of the River Elbe (Střekov, Czech Republic) from spring to fall 2003 and 2004. The effect was examined separately for immature (up to 2 years old) and adult fish and also the most abundant species (roach Rutilus rutilus, bleak Alburnus alburnus, chub Squalius cephalus, gudgeon Gobio gobio). More than 13 thousand fish from 23 species were recorded in the fishpass during both years. The highest levels of fish occurrence in the fishpass were observed during the spring spawning migrations of adults (April-May) as well as during the late summer and fall migrations of adult and immature fish (September-November). While the total number of both fish age categories was significantly related to the interaction of water temperature and flow, however, responses of individual species and age categories differed from each other. The numbers of adult bleak, chub and gudgeon increased with higher temperature. The maximum numbers of adult bleak migrated at medium values of temperature (15-20 °C) and flow (140-270 m3 s–1). The abundances of adult chub and adult plus immature gudgeon were higher with higher flow. The numbers of immature bleak and chub decreased with increasing flow. The numbers of adult and immature roach were influenced only by water flow with maximal numbers migrating under medium values of flow. Generally, we observed that immature fish and small- and middle-sized species required lower values of water flow than adult fish or large species to facilitate their movement. The exception was gudgeon, which required higher values of flow for its migration, a feature that could be related to its bottom dwelling nature or rheophily.