Any factor which impacts surface water and groundwater quality in the vicinity of the caves' recharge area can ultimately impact the survival of C. aculabrum and other cave creatures. Crayfish must have dissolved oxygen in the water for respiration. Severe water contamination by sewage, animal waste, gasoline, or a number of other materials, may result in seriously depleted oxygen concentrations and suffocation of cave crayfish. Contamination by toxic compounds, including heavy metals, many organic chemicals, and pesticides can be lethal to aquatic cave fauna, including crayfish. Sedimentation can clog gills, damage or destroy breeding habitat, and harm invertebrates upon which crayfish feed.
Residential development is the primary threat to the Bear Hollow Cave crayfish population.
Both cave sites have been vandalized and disturbed frequently in the past. The entrances to Logan Cave have been purchased by the Service and access is restricted. Despite protection afforded the cave, refuge staff estimated 10 cases of trespass for the period from April-July 1995. Logan cave is monitored by a light sensitive device located inside which records the time and date when activated but it is not regularly checked nor maintained. It is unknown when the gate vandalism occurred since there is currently no one scheduled nor responsible for monitoring cave trespass.