From Tolkien Gateway

Water-lilies were water flowers known for their round, flat leaves floating on the surfaces of ponds and quiet rivers. Their flowers can be of many colours, but Goldberry the River-daughter seems to have had a particular interest in white lilies. Tom Bombadil travelled to the lower reaches of the Withywindle to gather white water-lilies for her, and it was while returning from a lily-gathering expedition that he discovered Frodo and his companions, and rescued them from Old Man Willow.[1] Goldberry seems to have used her lilies to recreate her original home in the river: when Tom brought the Hobbits back to his house, they found a seated Goldberry surrounded by water-lilies floating in pots of earthenware.[2]

Like many other types of plant and flower, water-lilies were also known to grow in the verdant lands of Ithilien by the River Anduin. Long after their adventure with Tom and Goldberry, Frodo and Sam found their broad leaves floating in a quiet stream running down to the Great River.[3]

In the poem The Adventures of Tom Bombadil it appears that Tom first met Goldberry when she pulled him by his beard under water-lilies in the Withywindle River.[4]