Nine stratigraphic sections, each ≈5 m thick, were sampled from the Alamogordo Member limestones of the Lake Valley Formation, Sacramento Mountains, New Mexico, USA. Four stratigraphic sections consist entirely of lime mudstone and wackestone, whereas the other five sections have a prominent layer of crinoidal packstone about 1 m thick at their base. Stable isotopic analyses reveal that the lime muds in the sections with basal packstone layers show a downward decrease in δ18O and constant δ13C values, whereas those in the sections solely composed of lime mudstone and wackestone have, in general, relatively uniform δ18O and δ13C values. The diagenesis of the Alamogordo Member limestones was previously believed to have been governed by the downward percolation of meteoric water from a regional pre-Pennsylvanian exposure surface ≈100 m above this unit. However, the uniform δ13C and downward decrease in δ18O values in the lime muds in the sections with basal packstones indicate that the meteoric water ascended within the Alamogordo Member, rather than descended from the overlying exposure surface. This indicates that the basal packstones were probably a conduit for meteoric water. This is further supported indirectly by the relatively uniform δ18O and δ13C values of the lime mud in the sections without basal packstones. The implications are that the oxygen isotopic gradients may be used to identify palaeoaquifers, flow directions within these aquifers and that meteoric diagenesis below an exposure surface could be governed by flow through a palaeoaquifer.