Contamination of microalgal cultures by rotifers is known to cause large losses in productivity. The factors that control population dynamics of rotifers in microalgal cultures were studied in controlled contamination experiments in laboratory cultures. These experiments revealed that rotifer growth rates increase with microalgae biomass at low rotifer population densities and declines with rotifer biomass as the rotifer population approaches a carrying capacity. Experimental results were used to construct a model that describes the impact of rotifer contamination on three types of large-scale microalgal cultures. The results of this model indicate that rotifer contamination causes a complete loss in productivity in open pond and closed photobioreactor cultivation systems. In contrast, losses in productivity are limited in thin layer cascade reactors because the rotifer population cannot achieve a sufficiently high population density to cause a crash of the culture. These results suggest that different cultivation systems respond differently to rotifer contamination.