Research was carried out on fruits and seeds of Nymphaea and Nuphar taxa collected from Poland, Latvia and Estonia. The aim of the research was to establish diagnostic features which could enable identification of the examined taxa on the basis of the fruit and seed structure and creating a key to identify them. The examined organs were observed through an optic microscope and scanning electron microscope (SEM). New diagnostic features were discovered: spotting of fresh pericarp, the range of the fruit shape coefficient, the colour of the rays in the fruit stigma disc, the thickness of the seed testa, ribs in the seeds, and occurrence of the “puzzle shaped” cells on the surface of the testa. The discovered features were used in the taxonomic characteristics.