It was formerly considered to be related to the grasses and sedges (order Poales), but has been reassigned to the order Nymphaeales as a result of DNA and morphological analyses showing that it represents one of the earliest groups to split off in flowering-plant phylogeny, rather than having a close relationship to monocots, which it bears a superficial resemblance to due to convergent evolution.

Individual species are cosexual (with several types of hermaphroditic conditions) or dioecious, and are either wind-pollinated (anemophilous) or self-pollinating (autogamous).

Even as recently as 2003, the APG II system assigned Hydatellaceae to the grass order Poales in the commelinid monocots.

However, research based on DNA sequences and morphology by Saarela et al. indicates that Hydatellaceae is the living sister group of the water lilies (Nymphaeaceae and Cabombaceae) and thus represents one of the most ancient lineages of flowering plants.

As aquatic herbs, Hydatellaceae have environmental adaptations leading to derived characteristics that create a morphological similarity to the more distant taxon.