The water lilies (Nymphaeaceae) have been investigated systematically for decades because they are believed to represent an early group of angiosperms with relatively unspecialized floral organization. Although this group is small taxonomically, the relationships among genera of water lilies have eluded clarification and no single classification has become widely accepted. We present a well-corroborated phylogeny of water lily genera that is based on agreement between non-molecular data and DNA sequences obtained from both organellar and nuclear genomes. For specific portions of the resulting phylogeny, we evaluate the support conferred by each separate data set in comparison to various combinations. This approach enabled us to assess the potential benefits of further data acquisition, and also allowed us to evaluate the fundamental advantages and disadvantages of each data partition. Every data set contributed differently to the overall phylogenetic analysis and resolution of the cladogram. The 18S rDNA performed the most poorly, with homoplasious sites confounding some topological assessments in comparisons of closely related genera. However, as taxonomic distance increased, phylogenetic signal in the 18S rDNA data increased due to the expression of sequence variation in highly conserved sites. Even the 18S rDNA data were relatively congruent with the other data evaluated, and the resulting combined data analysis rendered a single maximum parsimony tree with strong nodal support throughout. When floral features were evaluated using this well-corroborated phylogeny, the pleiomerous condition of water lily flowers showed several instances of secondary derivations. Although the actual morphological details of the first water lily flowers remain uncertain, it is clear that the flowers of extant water lilies do not necessarily depict the ancestral organization. Results of the phylogenetic analysis are used to encourage the adoption of an evolutionarily based classification system for water lilies.