Hydroperiod length has been identified as a major driver in community assembly in freshwater systems. Yet we generally lack an understanding of how morphological traits respond to water level decrease under natural conditions. Here, we studied variation in body size and shape in lateral view in tadpoles of Scinax squalirostris and Odontophrynus americanus inhabiting ponds in superhumid highland plateau in southern Brazil. Hydroperiod did not affect tadpole size in either species. In relation to body shape, S. squalirostris tadpoles from long hydroperiod ponds had shorter tails and deeper tail fins than tadpoles from other hydroperiods. Predator presence was positively associated with hydroperiod, restricting our ability to separate their effects on tadpoles morphology. For O. americanus, tadpole shape was not affected by pond hydroperiod. We demonstrated that, in natural environment, the influence of hydroperiod on tadpole morphology might depend on species-specific characteristics, such as behavior and life-history traits. Our results indicate that local context may lead to different effects of hydroperiod, and hydroperiod alone can only partly explain the variation on tadpole shape.