The intensity of malaria transmission is often measured by looking at the fraction of individuals infected at a given point in time. However, malaria infections in individuals are dynamic, leading to uncertainty about whether a cross-sectional survey that represents a single snapshot in time is a useful representation of a temporally complex process. In this analysis, we examine the impact of parasite density fluctuations on the measurement of parasite prevalence. Our results show that parasite prevalence may be underestimated by 20% or more, depending on the sensitivity of parasite detection.