Durham Wildlife Trust says the foot-and-mouth outbreak has had such a devastating effect on visitor numbers it is now £24,000 in debt.
The trust depends on school trips and visitors to its nature reserves bringing in money.
However, visitor centres at Low Barns, Witton-le-Wear, and Bowlees, near Middleton-in-Teesdale, County Durham, were both closed from February 23, losing out on visits by an estimated 3,000 children.
Low Barns nature reserve also ended up housing cattle and sheep which had been brought in to temporarily graze the area.
Trust chief executive Richard Wood said rare flowers and wildlife was at risk because conservationists have been unable to carry out essential maintenance, such as clearing scrub.
Mr Wood said: "We maintain some of Hannah Hauxwell's meadows in Upper Teesdale, which are among the finest in the country but need to be grazed at certain times of the year to help rare flowers reseed, but we haven't been able to do that.
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