There is increasing recognition of the importance of rapid adaptation in the dynamics of populations and communities. While the effects of rapid adaptation on the stability of populations have been shown in experimental systems, demonstration of their impacts in natural populations are rare. We examined the relationship between clonal dynamics and population stability of natural Daphnia pulex populations experiencing seasonal environmental variation. We show that the degree of asynchrony in a population's clonal dynamics is tightly linked to its population-level stability. Populations whose clonal abundances were more asynchronous were more stable temporally. Variation in asynchrony was related to variability in primary productivity, and experiments using clones from the study populations revealed significant genotype by environment interactions in response to food level. This suggests that clonal turnover was not due to neutral dynamics alone but may be linked to variation in functional traits associated with resource acquisition and conversion.