We don't know.
The ultimate fate of the Entwives, and the reason for their mysterious disappearance eons ago, are never definitively explained in the text of The Lord of the Rings, the appendices, or any of the supplementary material of Tolkien's legendarium. The closest Tolkien ever comes to addressing this is in one of his letters to a fan, which I quote as follows (emphasis added):
[Tom Bombadil] has no connexion in my mind with the Entwives. What had happened to them is not resolved in this book. [Bombadil] is in a way the answer to them in the sense that he is almost the opposite, being say, Botany and Zoology (as sciences) and Poetry as opposed to Cattle-breeding and Agriculture and practicality.
I think that in fact the Entwives had disappeared for good, being destroyed with their gardens in the War of the Last Alliance (Second Age 3429-3441) when Sauron pursued a scorched earth policy and burned their land against the advance of the Allies down the Anduin (vol. II p. 79 refers to it). They survived only in the 'agriculture' transmitted to Men (and Hobbits).
Some, of course, may have fled east, or even have become enslaved: tyrants even in such tales must have an economic and agricultural background to their soldiers and metal-workers. If any survived so, they would indeed be far estranged from the Ents, and any rapprochement would be difficult – unless experience of industrialized and militarized agriculture had made them a little more anarchic. I hope so. I don't know.
-- The Letters of J.R.R. Tolkien, Letter #144
Note that, in true Tolkien style, he is still writing from an "in-universe" point of view, never acknowledging himself as the creator of these fictional worlds and characters, but rather reporting on information "available to him" which may be incomplete or inaccurate.
By writing this ambiguously bittersweet response, Tolkien maintains the mystery and the pathos of the Entish species. He could have written that Sauron destroyed all the Entwives, or that they ultimately came back home to the Ents, or even that most of them were killed but eventually a few returned to ensure the survival of the Entish line. Instead, he deliberately left the question open, so that fans of the book (even those who set store in extratextual authorial commentary as "canonical") can choose their own preferred ending to the story of the Ents and Entwives. There's a whole range of possibilities, ranging from tragic to hopeful:
- they and their gardens were all destroyed in the Second Age;
- they, or at least some of them, fled or became enslaved;
- the survivors became so estranged from their roots (pun intended) that, even if the Ents found them in future, they would find it hard to reconcile;
- there might be hope for a reunion of spirits in the future.
It's up to you which one you'd like to go with or accept as "headcanon".
Fair disclosure: this answer was largely inspired by an existing answer to the same question on another SE site.