Two different levels of certainty meet at Qumran, and it is worth keeping them apart.
The scrolls. From 1947 onward, some nine hundred manuscripts were recovered from eleven caves near the site, including copies of every book of the Hebrew Bible except Esther, a thousand years older than any previously known, alongside sectarian rule-books, hymns and commentaries. Their value to the study of the Bible and of Second Temple Judaism is not in dispute; they are the manuscript find of the century.
The settlement. What is disputed is the ruin beside the caves. Roland de Vaux, who excavated in the 1950s, read it as the communal home of a celibate ascetic sect, usually identified with the Essenes of Josephus and Pliny, who withdrew to the desert to keep a purity they thought the Jerusalem priesthood had lost. He pointed to a room he called a scriptorium, to many ritual immersion pools, and to a cemetery of austere single graves.
The alternatives. Other scholars have read the same stones as a fortified estate, a pottery works or a country villa, and have asked whether the scrolls were written here at all, rather than carried out from Jerusalem and hidden in the caves before the Roman advance of 68 CE that destroyed the site. There is no consensus. The atlas treats the Essene reading as the leading hypothesis and marks it as such, rather than presenting a contested interpretation as a settled fact.