Different physical factors such as solar radiation and wind impose strong vertical gradients in lake water columns and have important consequences on the distribution of aquatic organisms, from bacteria to fish. The heterogeneous vertical distribution of zooplankton in lakes is a clear example of a pattern related to these vertical gradients. Although the vertical distribution of zooplankton is probably controlled by multiple factors including light, resources, and predation, we still lack an integrated view of the interplay among these potential drivers, which are most often analysed separately. Moreover, most studies focussed on temperate lakes in which both phytoplankton resources and predation risk from fish are highest in the epilimnion, whereas only a few investigated boreal lakes, where phytoplankton is often more abundant in the metalimnion than in the epilimnion and cold‐stenothermic fishes prey on zooplankton below the warm epilimnetic layers. Here we investigated zooplankton vertical distribution in the epi‐ and metalimnetic waters of 17 boreal lakes that varied in fish predation, resource quantity and quality, and optical properties. The lakes were sampled at midday and midnight at five different depths in the well‐lit epi‐ and metalimnetic layers, where the strongest gradient in light (and predation risk) were expected. We used a multi‐model inference approach combined with linear modelling to examine the relative effects of physical factors (light attenuation, temperature and moon phase), resources (chlorophyll‐a and polyunsaturated fatty acids), and predation (fish and Chaoborus) on depth selection in four zooplankton taxa. All taxa showed a heterogeneous vertical distribution that in most cases had a clear diel migration pattern. Both predation and resources (food and temperature gradient) were associated with vertical depth selection by zooplankton, but each taxon had different responses to each factor. Vertebrate predators were associated with the vertical distribution of Daphnia, Calanoida, and Cyclopoida, but—unexpectedly—all these taxa reduced their diel vertical migration patterns in the presence of fish. Invertebrate predators were better correlated with the distribution of Cyclopoida, which tended to be shallower when Chaoborus was abundant. Food abundance seemed important for Holopedium glacialis and Calanodia, while the temperature gradient was partly associated with both Daphnia spp. and Calanoida distribution. Finally, we found an intriguing, albeit weak, positive association between the vertical distribution of Cyclopoida and that of food quality. These results showed that taxa less vulnerable to predators such as H. glacialis perform inverse DVM, and that this is at least partly related to moon phase rather than to fish predation. They also suggest that boreal lakes colonised by stenothermic planktivorous fish behave differently from the classical DVM paradigm, given that visual predators do not have access to fully lit layers.