Ecological consequences of global warming include shifts of species ranges toward higher altitudes and latitudes as well as temporal shifts in phenology and life-cycle events. Evidence is accumulating that increasing temperature is also linked to reduced body size of ectotherms. While temperature can act directly on body size, it may also act indirectly by affecting the timing of life-cycle events and the resulting population age and size structure, especially in seasonal environments. Population structure may, in turn, be influenced by temperature-driven changes in resource availability. In a field mesocosm experiment, we investigated how water temperature and mixed surface layer depth (a temperature-dependent determinant of light availability to phytoplankton) affected population dynamics, population age and size structure, and individual size at stage (size at first reproduction) of Daphnia hyalina during and after a phytoplankton spring bloom. Mixed layer depth was inversely related to the magnitudes of the phytoplankton spring bloom and the subsequent Daphnia peak, but had no effect on the body size of Daphnia. Conversely, temperature had no effects on abundance peaks but strongly affected the timing of these events. This resulted in at times positive, at other times negative, transient effects of temperature on mean body size, caused by asynchronous changes in population size structure in cold versus warm treatments. In contrast to mean body size, individual size at stage consistently decreased with increasing temperature. We suggest that size at stage could be used as an unbiased response parameter to temperature that is unaffected by transient, demographically driven changes in population size structure.