Diel vertical migration (DVM) is a common behaviour of many pelagic zooplankton species. While the causes (mostly predator avoidance) and ecophysiological consequences of DVM for zooplankton have been well studied, little is known about the consequences of DVM for the pelagic food web. DVM creates a temporal and spatial grazer-free niche for edible phytoplankton, and theoretical models predict that parts of the phytoplankton community should use this niche. Conceivably, DVM could also cause nutrient transport between separated water layers. We experimentally investigated the influence of DVM of the zooplankton species, Daphnia hyalina, on the nutrient and phytoplankton dynamics of an oligotrophic lake. We used 10-m deep field enclosures with a 4-m deep, well-mixed surface layer. The enclosures contained either migrating or non-migrating Daphnia populations; temperature was kept nearly constant across the entire enclosure depth. Our results show that DVM had significant quantitative and qualitative effects on the phytoplankton community. There was no measurable net nutrient transport between hypolimnion and epilimnion. The gelatinous green alga Planktosphaeria gelatinosa, was the dominant algal species in our experiment. Its abundance decreased in DVM treatments, and thus also influenced the total biomass and diversity of phytoplankton communities.