Groundwater habitats in the Dinaric Karst are home to the only known cave-adapted genus of bivalve mollusks, which currently survives as three distinct species with a highly fragmented distribution. Over the past few decades, Congeria populations suffered a steep decline across their range, as a result of human activities. Here, we identify the most pressing issues concerning the current conservation status of Congeria and identify key priorities for its scientific study. The building of dams and other hydrotechnical constructions have led to a significant decrease in the water inputs that used to supply underground systems where Congeria lives, contributing to a reduction of the cave habitats feasible for bivalve settlement. This is relatively well documented in Popovo polje where, as a result of hydrotechnical interventions on Trebisnjica river, water level drop destroyed well over 99 % of Congeria kusceri population in Zira cave and caused their complete disappearance in other caves. Similar factors are likely to have also affected the sister species Congeria jalzici in the Lika region. In addition, the salinization of Neretva river, lack of proper wastewater management, intense agriculture, tourist exploitation, and additional hydrotechnical plans add to the ongoing decline of the quality of Congeria habitats. These threats are expected to least to drastic reductions in population size within the next few decades, and this situation might be further aggravated by the lack of regulations and active measures for Congeria protection, as well by the limited understanding of its biology. Future scientific studies should be aimed at better elucidating microhabitat preference, defining the range of tolerance of environmental parameters, and assessing the size and genetic viability of existing Congeria populations. However, we highlight that these efforts would most certainly require the collaboration of local authorities and the allocation of appropriate financial resources in order to be effective.