Climate change will increase the temperature of rivers and will lead to more extreme events, such as floods. Temperature increases and floods will likely alter the phenology of freshwater species differently and have the potential to significantly disturb prey–predator interactions. In spring, an increase in temperature triggers an increase in primary production and controls the timing of the emergence in brown trout (Salmo trutta L.). Hydrology regulates the abundance of invertebrates, which are the main food source for newborn alevins. As such, climate change may desynchronise the relationship between fish emergence and invertebrate production, resulting in a negative impact on the performance of newly emerged alevins. In the present study, we quantified the abundance of invertebrates and the performance (survival and growth) of newborn alevins in early spring (March) compared to late spring (April/ May) in 8 enclosures in a semi-natural channel. In addition, we simulated a flood in 4 enclosures in late spring. Our results revealed that survival and growth of alevins in early spring were limited due to low invertebrate abundance. In late spring, there was a decrease in the survival of alevins placed in the flooded enclosures, likely due to the reduction of food availability. However, the growth of survivors increased, probably because of the increase in the abundance of Chironomidae after the flood and a reduced competition between congeners. Our results demonstrate that when emergence and flooding happen simultaneously, they can limit resources which will impact the survival and growth of young salmonids in running waters