Atlantic salmon deposit their eggs in redds within the river bed during late autumn. Eggs mature in the gravel during winter with hatching and alevin development occurring in early spring. These early life stages, located in the hyporheic zone, are exposed to surface-groundwater interactions and may be dependent on subsurface influx during regulated low flows for survival. Two recent studies, one in a seasonally regulated river and one in a river exposed to hydropeaking, displayed unexpectedly high survival of eggs in surface dewatered areas because of the influx of oxygenic subsurface water. This paper documents the results of field observations on newly hatched alevins in the same two study areas. Newly hatched alevins proved to be more sensitive to surface dewatering than the eggs, showing a higher mortality. Shorter periods of surface dewatering in the river with hydropeaking resulted in higher alevin survival compared to the seasonally regulated river, when still permanently drained after egg hatching. The duration of exposure to dry conditions in drawdown areas is highlighted as key for alevin stage survival, but a strong emphasis should be put into considering all life history stages when implementing environmental flow strategies, as well as taking into account the extent of groundwater influx and the potential for flexible hydropower operations.