As its name suggests, Lake Cave is renowned for its crystal-clear water, which not only creates beautiful reflections of the dazzling crystal cave formations but also serves as a habitat for endangered species of stygofauna. These microscopic aquatic animals live within the cave and survive by eating whatever drifts their way, be it decomposing insects, tree roots, or small debris. Most of these stygofauna measure less than a millimetre in length, and have become adapted to the darkness, lacking both eyes and pigmentation. It is possible that some of these species are unique to Lake Cave.
The water within the cave originally falls as rain to the east of the coastal limestone ridge. That rainwater is absorbed into the ground and then moves through the many cracks, fissures and caves in the porous limestone until it reaches the coast. The quantity of water entering the ground and passing through the limestone directly affects the lake’s water level within the cave.
In the early 2000s, water levels began to significantly decrease, posing a threat to the survival of the stygofauna and diminishing the prominence of the iconic crystal reflections. Since 2010, the Margaret River Busselton Tourism Association, which has since established the Capes Foundation, launched an extensive monitoring and research program aimed at recording and explaining the changing cave water levels.
Through this research, it became evident that the type and intensity of surface vegetation in the catchment to the east of the limestone ridge was having a major influence on the amount of groundwater entering the limestone system and flowing through caves, such as Lake Cave. Patterns in the growth and harvesting of nearby blue gum plantations also suggest a link to changing water levels.