Changes in the near-bottom abundance of zooplankton on scales of centimeters to meters and hours to seasons are of great importance to corals and other benthic zooplanktivores. Our objective was to characterize such spatio-temporal changes over several coral reefs in the Gulf of Aqaba, Red Sea. Using arrays of underwater pumps, we found a substantial depletion of zooplankton near the bottom. Vertical gradients in zooplankton abundance were steeper during the night than day, mostly due to a greater nocturnal increase in zooplankton biomass higher in the water column. On average, the layer 200 μm) zooplankters around dusk and their disappearance in the morning. Diurnal predation by zooplanktivorous fish, sediment resuspension by benthivorous fish and zooplankton behavior appear to control the dynamics of suspended particles over the reef, creating sharp vertical gradients and a remarkable diel cycle in the ratio between nutritious plankton and inorganic particles.