The irreplaceable books and manuscripts, some dating back to medieval times, were becoming damp because of holes in the rectory roof where rain was coming in.
Now, English Heritage has donated £65,000 for much-needed repairs to the roof and guttering of the cathedral's rectory and Librarian's Loft, where thousands of extremely rare and valuable books are kept.
When cathedral architect Christopher Downs carried out an inspection, he made the alarming discovery that mould was growing on some of the precious library books.
The cathedral's assistant librarian Joan Williams, said: "The Refectory – where the monks once ate their meals – was converted to a library in the late 1600s and houses the cathedral's early printed books dating from 1500 up to 1850.
"There are about 20,000 volumes as well as important antiquarian manuscripts and music collections.
"Ancient books and manuscripts can deteriorate very rapidly in damp conditions, so it is vital the roof repairs are carried out as quickly as possible.
"We have already had to cover two of the bookcases with polythene sheets where water comes through the roof after very heavy rain."
Since 1991 English Heritage has contributed more than £1million to repair projects at Durham Cathedral.
Carol Pyrah, regional director of English Heritage for the North East, said: "Durham Cathedral is one of the most important and best-loved buildings in the region and forms a major part of the World Heritage Site. We are delighted to be supporting the cathedral.
Durham Cathedral's Dean, The Very Reverend Michael Sadgrove, said: "This grant is extremely good news both for the cathedral and for scholars who use the library. Once again we are indebted to English Heritage for their indispensable support."
This is the 16th round of grants since English Heritage's Cathedral Grants scheme was launched in 1991 and five other cathedrals across the country have been offered awards between £51,000 and £100,000 to carry out repairs.