We studied the habitat choice of juvenile and adult Daphnia pulicaria in thermally stratified water columns (plankton towers) with a deep water algal maximum (DCM). The DCM consisted of either filamentous cyanobacteria (Planktothrix agardhii), non-filamentous Chlorophyceae (Scenedesmus obliquus) or a mixture of both. Adult D. pulicaria spent more time at colder temperatures in the presence of P. agardhii than in the presence of S. obliquus, either as the sole food source or when mixed with P. agardhii. Juvenile D. pulicaria did not show a different habitat choice in the three food treatments. In a fourth treatment, we also determined Daphnia distribution in the absence of food. Comparing the habitat choice of juveniles and adults in each of the four treatments, the latter spent more time at colder temperatures when food was absent or when in the sole presence of P. agardhii. Additional grazing and stable isotopic marker experiments showed that D. pulicaria ingested and assimilated Planktothrix filaments. The results suggest that the differences in habitat choice between adult D. pulicaria in the presence of different food types were influenced by food quality effects: adult Daphnia which move to colder waters in the presence of low quality P. agardhii decrease their metabolic rate and might thus be able to invest more resources into reproduction when environmental conditions improve.