The source area of groundwater for springs discharging from lithologically variably perched aquifers is essential to understand when establishing baseline aquifer characteristics. Stratigraphic data from hydrostratigraphic outcrops and geochemical data from springs were used to characterize the hydrogeology of a remote, data-poor aquifer. This study focuses on the hydrogeological variability within the shallow karst-siliciclastic Coconino (C) aquifer on the Kaibab Plateau, north of Grand Canyon National Park. Stratigraphic data were collected from 8 locations, and 22 C aquifer springs were sampled for 18 months. Stable isotope analyses indicate that groundwater is biased to winter recharge in the form of snow and shows similar isotopic signature for groundwater storage areas for all C aquifer springs. Stratigraphic analyses show that the primary water-bearing unit in the C aquifer thins dramatically from south to north and has evaporite lithofacies directly above the unit. Principal component analysis (PCA) indicates that the hydrogeochemistry is influenced by SO42−, Cl−, Mg2+, Ca+, specific conductivity, alkalinity, and δD variability. The stratigraphic variability influences geochemistry at multiple locations and has geochemical variabilities that correlate with changing lithology. Based on the PCA results, groundwater sub-basins were delineated based on geochemical variability. This study provides new analytical tools for land managers and karst hydrogeologists to evaluate lithologically complex aquifers by evaluating the stratigraphy and with high-resolution data. Cost-effective stratigraphic analyses and high-resolution spring sampling can and should be used to evaluate lithologically complex aquifers in remote, data-poor regions.