Flowers, branches, or stems that were picked before Shabbat for their beauty or fragrance, are not muktzeh on Shabbat. Therefore, a vase containing branches that are used for their beauty or fragrance may be moved. Similarly, they may be removed from the water for viewing or smelling. There is no problem of Kotzer, since there are no roots. One may also return stems to the water if they do not have flowers, or if they have fully-developed flowers. There is no problem of Zore’a, since the water will not cause any further growth but will only preserve their freshness so they do not wither.
However, one may not place in water any stems with flowers that are budding or that have not yet fully opened, because placing them in the water causes further growth. Nevertheless, one may remove them from the water. This is not considered Kotzer, because they have not put down roots in the water. Once removed, though, one may not replace them. Therefore, if one receives a bouquet of flowers as a gift on Shabbat and it contains flowers that have not yet fully opened, one may not place them in water, as this will cause the flowers to grow and open. Rather, one should put the bouquet in a vase that does not contain water.