Marsileaceae is a unique family of semi-aquatic ferns mainly growing in seasonal wetlands worldwide. These habitats present several challenges, since plants go from being wholly submerged to being exposed to aerial conditions, increasing drought stress. Although heterophylly has been studied as an adaptation to these environmental changes, there are still many unanswered questions concerning the mechanisms underlying the ecology of Marsileaceae. We studied the presence of circadian regulation in stomatal conductance, carbon assimilation rate, intrinsic water-use efficiency (iWUE), and leaf movement of four species from all three genera of Marsileaceae, and related our findings to possible water stress adaptations. No circadian regulation was detected in Pilularia globulifera, whereas Regnellidium diphyllum and two Marsilea species had an apparent rhythm in their stomatal conductance and iWUE, with species-specific patterns. Moreover, light-independent leaf movement was only found in Marsilea species. Taken together, the rhythm in iWUE and leaf movement, along with other anatomical traits for conserving water, infers different strategies to either increase carbon gain or reduce water use in Marsileaceae. Our study represents the first steps towards understanding the underlying drivers and adaptive value of circadian regulation in this family.