Rotifer preference for the upper (0–2 m) or deeper layer (5–35 m) of the water column was assessed at midday and midnight in an oligotrophic mountain lake during summer, and related to temperature, food availability, presence of predators and exposure to solar ultraviolet radiation (UVR). Whereas Keratella cochlearis and Synchaeta pectinata showed a population maximum in the deeper layer during midday and in the upper layer during midnight, Asplanchna priodonta, Synchaeta kitina and Filinia terminalis always remained in the deeper layer. In contrast, Polyarthra dolichoptera and S. grandis were the only rotifer species that remained in the upper layer. Possession of mycosporine-like amino acids, a family of photoprotective compounds seemed to be an important strategy for occupying the upper layer. For other species, midday positioning in the deeper layer seemed to be related to UVR avoidance rather than to predation pressure, whereas the upward shift at night was species-dependent. Migrating species seemed favoured by higher temperatures in the upper layer, whereas non-migrating species seemed restricted by factors such as food supply. Our study indicates that rotifers exhibit different species-specific strategies for dealing with factors such as UVR exposure, temperature and food availability.