The karst disturbance index (KDI) consists of 31 environmental indicators categorized within the five broad categories of geomorphology, hydrology, atmosphere, biota, and culture. This article discusses the application of the KDI to the rural karst region of Waitomo, New Zealand. Previous applications of the KDI measured disturbance to urban areas as delineated by geo-political boundaries while this study used a physical boundary of a small karst catchment. Such an approach ensures greater environmental specificity of measured disturbance levels compared to those determined according to arbitrary, politically defined areas. The study included a comparison of a local resource manager and a visiting karst expert's determinations of disturbance levels for the catchment. Overall, the Waitomo catchment was found to be moderately disturbed. The only significant, direct disturbances were deforestation and erosion; however, these lead to the indirect disturbance of cave biota, water quality and accelerated sedimentation of the catchment's waterways. We have a high degree of confidence in the validity of these results due to the ability to assess all of the applicable indicators in the index, and the consistency of scoring by both individuals who applied the index. The benefit of applying the KDI at the catchment level is the greater accuracy measuring disturbance as opposed to applying the index within geo-political boundaries that incorporate both karst and non-karst terrains. With disturbance data for a highly specific area, the Waitomo resource managers have the improved ability to effectively identify, target, remediate, and manage human disturbance of the karst landscape.