Abstract The Kaibab Plateau and Grand Canyon National Park in the USA contain both shallow and deep karst systems, which interact in ways that are not well known, although recent studies have allowed better interpretations of this unique system. Detailed characterization of sinkholes and their distribution on the surface using geographical information system and LiDAR data can be used to relate the infiltration points to the overall hydrogeological system. Flow paths through the deep regional geological structure were delineated using non-toxic fluorescent dyes. The flow characteristics of the coupled aquifer system were evaluated using hydrograph recession curve analysis via discharge data from Roaring Springs, the sole source of the water supply for the Grand Canyon National Park. The interactions between these coupled surface and deep karst systems are complex and challenging to understand. Although the surface karst behaves in much the same way as karst in other similar regions, the deep karst has a base flow recession coefficient an order of magnitude lower than many other karst aquifers throughout the world. Dye trace analysis reveals rapid, conduit-dominated flow that demonstrates fracture connectivity along faults between the surface and deep karst. An understanding of this coupled karst system will better inform aquifer management and research in other complex karst systems.