The spring of the Krupa river in southeastern Slovenia is the site of one of the biggest ecological disasters in the Dinaric Karst. Between 1962 and 1984 dozens of tons of pure polychlorinated biphenyls (PCBs) were dumped at the waste disposal sites and neighboring dolines by a local condenser factory. They were leached underground, and their concentration in spring water in the 1980s exceeded the US Environmental Protection Agency regulations by up to one thousand (Polič et al., 2000). The undegradable carcinogenic chemicals are still gradually released from the sediments into the groundwater and were detected in the tissues of the population of the olm (Proteus anguinus) residing in the aquifer (Pezdirc et al., 2011). The Krupa spring is also a presumed site of the very rare cave clam Congeria jalzici, although shells and not living animals were found in it (Hudoklin and Ilenič, 2012). Environmental DNA assay for Congeria is being developed to establish if a living population is present behind the spring and to survey the area for additional sites inhabited by the mollusk.