Changes in the water level of lakes, either natural or man-made, are important environmental perturbations for eulittoral benthic fish communities. In outdoor mesocosm experiments, we tested the effects of decreasing shelter availability due to autumn lake level decrease on the behavior and the growth of two littoral benthic dwellers, the juvenile burbot and the stone loach. The two species showed significantly different changes in behavior when shelter availability decreased. Burbot built up a distinct hierarchy when shelter became sparse with larger fish being significantly more successful in competing for suitable shelter than smaller conspecifics. The hierarchy however ceased when shelter availability decreased below a certain level. The largest fish then increasingly abandoned shelter use while smaller fish persisted their sheltering behavior. Stone loach, in contrast, showed no hierarchical order or size-related shelter use. However, both species showed a significant relationship between their ability to occupy their preferred shelter and their somatic growth. These two species provide an example of different strategies to deal with environmental perturbations like lake level decrease, with the stenoecious, dominant strategy of the burbot and the euryoecious, evasive strategy of stone loach. The results demonstrate the importance of conducting behavioral studies under as natural conditions as possible.