Throughout the book, the narrator makes references to or compares women to flowers. For example, the Commander and Serena Joy's house is completely doused in floral imagery: there's a "watercolor picture of blue irises" (2.4) in the narrator's room; the bathroom is "papered in small blue flowers, forget-me-nots" (12.1); the master bedroom is decorated with "a starry canopy of silver flowers" (31.46). The first thing the narrator finally works the nerve up to steal is a daffodil from one of Serena Joy's arrangements. Even Jezebel's, where the Commander takes the narrator, is decorated with flowers. Flowers are also used to disguise things that are ugly or terrifying; the narrator compares the bloody mouth of a hanged man, for example, to the "red of the tulips" in Serena Joy's garden (6.26).
Flowers are often considered symbols of beauty or fertility. In The Handmaid's Tale they're given special attention as objects that can bloom and grow at a time when few women can. From a technical standpoint, flowers are also the part of a plant that hold the reproductive organs. They're constant reminders of the fertility that most women lack.
It seems the older Wives are seeking to hang onto their attractiveness and fertility by decorating themselves with flowers and tending gardens: "Many of the Wives have such gardens, it's something for them to order and maintain and care for" (3.2). Serena Joy takes a bizarre pleasure in mutilating flowers: when the narrator sees her chopping them awkwardly, she wonders, "Was it [...] some kamikaze, committed on the swelling genitalia of the flowers? The fruiting body" (25.25). Perhaps these are attacks Serena Joy would like to make on the Handmaid, who can be seen as a flower living in her house.