Ground-based hyperspectral imaging is useful for geologic mapping because of its high spectral and spatial resolutions at a millimeter to centimeter scale. We have used hyperspectral and terrestrial laser scanner (TLS) data collected in close range to a roadcut near Jane, Missouri, that contains a subvertical outcrop of Lower Mississippian limestone. The outcrop consists of the Compton, Northview, and Pierson Formations, which we evaluated for facies heterogeneity. The sequence near Jane, Missouri, was deposited in shelf margin with high-frequency sea-level fluctuations. These fluctuations introduced lithologic and geometric heterogeneity to the facies, and debris flows brought in carbonate mounds referred to as outrunner blocks. These are important to interpret accurately because of their equivocal depositional origin, which is highly debated by previous workers. We combined hyperspectral data with TLS for an integrated spatial analysis of geometric and compositional variations in facies by accurate, point cloud-registered mineralogical mapping. We mapped several carbonate facies based on spectral signatures of calcite, silt, and clay particles and distinguished pure limestone outrunner blocks from surrounding mud-prone limestone facies with various proportions of silt and clay (a total of approximately 60%). By tracing the classified facies from combined hyperspectral and TLS imagery, we produced a lithostratigraphic framework, which indicates rapid changes in lithology and the presence of shale baffles that vary the character of the Compton through Pierson interval and contribute to heterogeneity in this outcrop. The data suggest a lower energy depositional environment and support the hypothesis of transported outrunner blocks in a distally steepened ramp system. The information that we have evaluated in our study could help to explain reservoir heterogeneity in equivalent carbonate fields.