The widespread increase in the relative abundances of Cyclotella sensu lato taxa in Northern Hemisphere lakes suggests that these taxa are strong indicators of global change, yet the specific factors affecting the success of these species have been difficult to identify. The primary objective of this study was to investigate the interactive effects of temperature (7–10°C or 11–15°C), light (high or low) and nutrients (control or nitrogen plus phosphorus) on cell densities of various Cyclotella sensu lato taxa. We observed varying interactive effects of temperature, light and nutrients on Lindavia bodanica, Lindavia comensis, Lindavia ocellata and Discostella stelligera. For example, when nutrients were provided, Lindavia radiosa was more abundant under high light conditions, whereas L. ocellata was more abundant under low light conditions. The secondary objective was to determine whether different phytoplankton communities (one dominated by diatoms and the other by a mixed assemblage) altered the response of D. stelligera to abiotic factors. High temperature, light and nutrients only increased cell densities of D. stelligera when this species occurred in the diatom-dominated community. This study provides further ecological insight on Cyclotella species that serve as important indicators of environmental change.