"there have been toads shut up in rocks for thousands of years"
by cm
The Blois Toad found in a Flintstone, 1851
Public DomainThe Blois Toad found in a Flintstone, 1851

Van Helsing is referring to a remarkable but largely forgotten phenomenon: live frogs and toads supposedly found alive inside stones and coal.  More than 210 cases have been reported, but no satisfactory scientific explanation has been proposed. 

During the nineteenth century, regular stories about entombed amphibians appeared in the British press and scientific journals, so Bram Stoker's readers would have been well aware of the phenomenon.  Benjamin Franklin and Charles Dickens both wrote about the subject.  In the 1820s, geologist William Buckland ran a series of experiments to test the idea that toads could survive indefinitely in rock.  He sealed a number of toads in holes in blocks of sandstone and limestone.  After a year, the toads in the sandstone were all dead, but some of those in the more porous limestone were still alive.  After a second year, all were dead. 

An entertaining article on entombed toads can be found here.