Zooplankton that are vulnerable to predation by planktivorous fish typically remain in deeper, darker water during the day. Vertical position may be affected by profiles of temperature and oxygen concentration, but light levels are thought to be critically important. Water transparency in temperate lakes is strongly dependent on the concentration of dissolved organic carbon (DOC). Therefore, different patterns of zooplankton vertical position might be expected in lakes that vary in their level of DOC. The importance of three factors (light, temperature and oxygen) that might affect vertical position of major zooplankton groups was evaluated in 10 small lakes located in central Ontario. The lakes, encompassing a wide range of water colour, were sampled in May, June and August of 2000. Small cladocerans were found to be always higher in the water column than large cladocerans, while copepods were deeper. Small cladocerans had a weak response to the predictive factors, but copepods and large cladocerans were strongly affected. The vertical position of copepods was consistently dependent solely on Secchi depth. Surprisingly, for large cladocerans, temperature gradient was decisive in May and June, and only in August was water transparency the most important variable. Overall, water transparency, as determined by level of water colour, was the most important variable but, depending on taxonomic group and time of year, temperature and oxygen were also major determinants of vertical position.