If someone has a mint plant in a cup of water for either replanting purposes and/or smelling purposes (freshness): Can it be removed on Shabbos, for smelling and then put back in the water?
It is permitted to take out the plant for the purpose of smelling it, and then to place it back in the water. This is true provided that there are no flowers; if the plant has (not completely opened) flowers, it is prohibited to place it back in the water, because this causes the flowers to open.
This is true provided the plant was initially placed in the water with the intention of using it for smelling on occasion. If the intention was to place it in water for ‘fresh storage’ and not to use it at all, the plant would be muktzeh, and may not be taken out.
See Shulchan Aruch, Orach Chaim 336:11, concerning the prohibition of placing wheat etc. in water. The Rema permits placing plants in water, but quotes siman 654 (1), where it is only permitted to put back a plant into water if it was already in water before.
See Chayei Adam (11:3) and Tosefos Shabbos (336:21) who write that it is only permitted to return a plant to water, whereas Shulchan Aruch Harav and the Peri Megadim are more lenient. The Mishnah Berurah (336:54) is stringent in this matter, and explains that the Rema only permits putting the plant back into water. This is also the ruling of Shemiras Shabbos Kehilchasah (26:26).
See also Yecheveh Daas, Vol. 2, p. 200 (lenient, based on Shulchan Aruch 221:11 and other sources).
The particular question deals with removing a plant from water, and placing it back, and this is permitted, provided there is no issue of muktzeh.