Hydric fluctuations in the Pantanal comprise annual dry and wet seasons that modify local diversity and plant morphology and anatomy. Widespread in this wetland are the sympatric Pontederia azurea and P. crassipes, which, although primarily aquatic, can also develop in non-flooded environments. This study undertook a comparative investigation of the qualitative and quantitative phenotypic responses and strategies of these two species (regarding life-form and leaf morpho-anatomy) in moderately dry and aquatic environments in the Pantanal. Field observations, conventional methods in plant anatomy, and leaf biometry were performed, followed by statistical analyses. Phenotypic responses, such as the decreased size of lacunae, increased lignification of vessel elements, and storage of starch granules, are the most prominent responses associated with moderately dry environments. The ability of petioles to elongate and inflate seems to be closely related to specific morphological patterns of each species. In contrast, petiole length, leaf blade dimensions, size of lacunae, and lignification rates seem to be somewhat associated with water level fluctuations. Our results provide evidence of how plant structure can simultaneously reflect phylogeny and ecology, thus supporting further investigations into phenotypic plasticity.