The interplay between functional traits and habitat associations drives species' evolutionary responses to environmental heterogeneity, including processes such as adaptation, ecological speciation, and niche evolution. Seasonal variation is an aspect of the environment that varies across habitats, and could result in adaptive shifts in trait values across the life cycle of a plant. Here, we use phylogenetic comparative methods to evaluate the joint evolution of plant traits and habitat associations in Lasthenia (Asteraceae), a small clade of predominantly annual plants that have differentiated into an ecologically diverse range of habitats, including seasonal ephemeral wetlands known as vernal pools. Our results support the hypothesis that there is a link between the evolution of leaf morphology and the ecohydrological niche in Lasthenia, and, in the formation of aerenchyma (air space), differentiation between vernal pool and terrestrial taxa is fine-tuned to specific stages of plant ontogeny that reflects the evolution of heterophylly. Our findings demonstrate how the relationships between traits and habitat type can vary across the development of an organism, while highlighting a carefully considered comparative approach for examining correlated trait and niche evolution in a recently diversified and ecologically diverse plant clade.