Impacts of land use activities on the water quality of a large karst spring (Blautopf, Germany) were identified by extensive spatiotemporal water quality analysis, and for the first time, a paired-catchment approach was successfully transferred to a subsurface karst and cave system. Water quality changes in karst springs are often rapid, strong, and influenced by a number of factors. This comprehensive study was performed by means of long-term (30-month) monitoring, intensive sampling during a rainfall event, and spatial sampling across the cave system. The spring showed moderate seasonal variations for most parameters but a strong response to the rainfall event, where fecal bacteria (E. coli) increased 120-fold, with a most probable number (MPN) of up to 17,168 per 100 mL. The catchment area (165 km2) was subdivided into two sub-catchments of similar size and morphology but differing in land use. The subsurface paired-catchment approach demonstrated that major ions, trace elements, rare earth elements and fecal bacteria differed significantly between both sub-catchments and could be attributed to different land use activities. Nitrate was linked to agriculture, whereas potassium, chloride, gadolinium, and fecal bacteria could be identified as indicators for wastewater effluents. Significant influences on water quality included winter application of road salt, (potential) sewer overflows and, to a lesser extent, nitrogen fertilization. This study underlines the susceptibility of karst springs to contamination and demonstrates the applicability of a subsurface paired-catchment approach as a promising tool to identify spatially resolved impacts of land use activities to a karst aquifer.