Climate warming can affect ecological food chains directly by increasing the rates of physiological processes and indirectly by changing habitat use and altering predator–prey interactions. In Lake Maggiore, Italy, a greater than 10-fold increase in the mean annual population density of Bythotrephes longimanus (Cladocera Onychopoda) was recorded between 1987 and 1993, when high values of the North Atlantic Oscillation winter index indicate warmer winter and spring temperatures across Europe. Bythotrephes remained abundant and further increased during the following 10 yr, as water temperature continued to increase. We analyzed changes in water temperature, timing of thermal stratification, and hypolimnion depth to test whether changes in the duration and thickness of a warm, low-light, deep-water refuge from fish predation can account for increases in the invertebrate predator’s abundance and seasonal duration. Using a 21-yr data set, we found that the sharpest increase in Bythotrephes abundance coincided with a shift from late August to May in its first appearance in the water column. The appearance of the planktonic population was, in turn, linked with earlier thermal stratification and earlier establishment of the predation refuge. The duration and thickness of the refuge increased as a result of earlier warming and deeper mixing, factors affected by climate rather than decreased water clarity. Daphnia hyalina galeata, the dominant grazer and a prey of Bythotrephes, decreased sharply as Bythotrephes increased. This study provides an example of how climate warming can indirectly affect the population density and phenology of a key invertebrate predator and, hence, the functioning of the pelagic food web.