Over the last four decades much progress has been made towards recognising causes of global amphibian declines, but knowledge of fine scale drivers, particularly for specialised species, remains poor, inhibiting conservation effectiveness. The case of the Table Mountain Ghost frog (Heleophryne rosei) provides an example of this, listed as Critically Endangered for the last 15 years with limited conservation actions identified due to a lack of information about threat mechanisms and magnitude of declines. To address this, we investigated H. rosei tadpole occupancy dynamics over three years in stream pools on Table Mountain in Cape Town, South Africa, the only locality where this species occurs. Tadpole spatiotemporal distribution was examined as a function of abiotic and biotic factors to quantify habitat requirements, rank threats, and identify conservation actions. Heleophryne rosei tadpole occupancy was negatively correlated with levels of fine sediments (silt and sand), which embed larger substrates and decrease the diversity of benthic microhabitat. Increased abundance of these fine sediments was also associated with higher extinction probabilities. Localised habitat degradation from hiking paths, alien vegetation, and flow manipulation were identified as the primary threats to this species, increasing the sources of fine sediments and inhibiting the fluvial systems ability to effectively flush these sediments out. Our results demonstrate the importance of pore space refugia for mountain headwater stream-adapted amphibians and provides the required data to inform management decisions for this Critically Endangered species.