The Holder Formation (Pennsylvanian, Virgilian) of southern New Mexico, USA, consists of limestones interbedded with siliciclastics. It was deposited during times of glacio-eustatic sea-level change and was exposed subaerially during multiple sea-level lowstands. Microcomponents and whole-rock samples of limestones were analysed for δ13C and δ18O values to examine the method of whole-rock isotopic analysis for detecting subaerial exposure events and to determine the diagenetic processes acting during subaerial exposure. Whole-rock isotopic shifts are not consistently present across petrographically identified subaerial exposure surfaces. Apparently, whole-rock isotopic shifts do not result from wholesale replacement of the host sediment during soil formation. However, the isotopic shifts are present in calcareous, soil-precipitated microcomponents, such as rhizoliths, laminated crusts, and soil-precipitated cements. The components are heterogeneous in isotopic composition, but converge on a meteoric calcite line at about δ18O=−5.5‰. These microcomponents are heterogeneous in distribution and may either dominate or be a minor constituent of the whole rock at a single stratigraphic horizon. Without petrographic selection of palaeosol components, the detection of whole-rock isotopic shifts may depend on the selection or chance sampling of a rock containing abundant microcomponents precipitated in a soil environment. Only minor whole-rock isotopic shifts come from those rocks bearing no evidence of exposure and bearing lithological characteristics suggesting subaerial exposure was unlikely.