Sometimes abrupt changes occur in nature. Examples of these phenomena exist in lakes, oceans, terrestrial ecosystems, climate, evolution, and human societies. Dynamical systems theory has provided useful tools to understand the nature of these changes. When certain non-linearities underlie system dynamics, rapid transitions may happen when critical thresholds for certain parameter values are overcome. Here we describe a malaria dynamical model that couples vector and human disease dynamics through mosquito infectious bites, with the possibility of super-infection, this is, the reinfection of asymptomatic hosts before they have cleared a prior infection. This key feature creates the potential for sudden transitions in the prevalence of infected hosts that seem to characterize malaria’s response to environmental conditions. This dynamic behavior may challenge control strategies in different locations. We argue that the potential for critical transitions is a general and overlooked feature of any model for vector borne diseases with incomplete, complex immunity.