Dormancy can serve as an adaptation to persist in variable habitats and often is coupled with sex. In cyclically parthenogenetic rotifers, an asexual phase enables rapid population growth, whereas sex results in diapausing embryos capable of tolerating desiccation. Few studies have experimentally tested whether sex–dormancy associations in temporary waters reflect evolution in response to the short hydroperiod selecting for diapause ability. Here, we demonstrate evolution of higher propensity for sex and dormancy in ephemeral rotifer cultures mimicking temporary ponds, and lower propensity in permanent cultures. Results are consistent with rapid evolution, with evolutionary changes occurring in a short timeframe (385 days, ≤ 84 generations). We also provide insight into mechanisms for rapid evolution in basal metazoans, discussing potential roles of new mutations, recombination and clonal selection.