The Nymphaeales currently includes three families and about 70 to 90 species.

The crown group of Nymphaeales has been estimated to be about 112 million years old.

The Cronquist system of 1981 recognizes the family but places it in the water lily order Nymphaeales.

At least 10 morphological characters unite the Nymphaeales.

This Hydatellaceae was placed among the monocots in previous systems, but a 2007 study found that the family belongs to Nymphaeales.

The exact relationships between Amborella, Nymphaeales and Austrobaileyales are not yet clear.

The family is part of the order Nymphaeales, which is one of the most basal flowering plant lineages.

The Angiosperm Phylogeny Website had since updated the Nymphaeales page to include the family.

Besides the mesangiosperms, the other groups of flowering plants are Amborellales, Nymphaeales, and Austrobaileyales.

Some earlier systems, such as Cronquist's system of 1981, often included the Ceratophyllaceae and Nelumbonaceae in the Nymphaeales.

The placement of Trithuria in Nymphaeales was a surprise to some but this position is supported by ten morphological synapomorphies:

Although, the Takhtajan system of 1980 separated the Nelumbonales, the new order was retained alongside the Nymphaeales in the superorder Nymphaeanae.

Together, these three families compose the order Nymphaeales in the APG III system of flowering plant classification.

If this interpretation is correct, Archaefructus may not be basal within angiosperms, rather it may be close to the Nymphaeales or the basal eudicots.

The orders Amborellales, Nymphaeales, and Austrobaileyales diverged as separate lineages from the remaining angiosperm clade at a very early stage in flowering plant evolution.

Most morphological and molecular analyses place Amborella, the nymphaeales and Austrobaileyaceae in a basal clade dubbed "ANA".

Nymphaeaceae is placed in the order Nymphaeales, which is the second diverging group of angiosperms after Amborella in the APG III-classification.

The exact relationship between these eight groups is not yet clear, although there is agreement that the first three groups to diverge from the ancestral angiosperm were Amborellales, Nymphaeales, and Austrobaileyales.

It was considered a relative of Nymphaeaceae and included in Nymphaeales in the Cronquist system but recent research has shown that it is not closely related to Nymphaeaceae or any other extant plant family.

Amborellales, Nymphaeales, Chloranthales, Petrosaviales, Trochodendrales, Buxales, Vitales, Zygophyllales, Picramniales, Huerteales, Berberidopsidales, Escalloniales, Bruniales, and Paracryphiales.

Trithuria (Hydatellaceae) diverged from the rest of Nymphaeales soon after Nymphaeales diverged from its sister taxon, which comprises all of the flowering plants except the two orders Nymphaeales and Amborellales.