Periodic variations in Earth’s orbital parameters force climate on local and global scales, with global responses particularly sensitive to the presence of ice sheets and their associated feedbacks. Therefore, determining whether orbital forcings influenced sedimentary records of the past, and if so, which had such an effect, can shed light on Earth’s climate sensitivity and global ice volume. To this end, we present a field- and drone-based cyclostratigraphy of the predominantly lacustrine El Molino Formation of the Late Cretaceous–Early Paleogene Potosí Basin in present day Bolivia, which contains carbonate mud parasequences that record fluctuating hydrological conditions, including ephemeral marine connections, from 73 Ma to 64 Ma. We introduce a novel methodology for incorporating drone imagery into a quantitative, three-dimensional stratigraphic model that generates an upward-younging quantity comparable to stratigraphic height, and we find that our model outperforms our own field measurements of stratigraphic height. We project drone imagery at two sites into the stratigraphic model to construct time series of outcrop color, which vary systematically with facies and track basin water depth. Spectral analysis of these time series reveals sedimentary periodicities corresponding to short eccentricity, precession, and semi-precession, which are corroborated with measurements of magnetic susceptibility from mudstones. We generate independent age models at both study areas from four new U-Pb chemical abrasion–isotope dilution–thermal ionization mass spectrometry (CA–ID–TIMS) ages, which are consistent with an orbital interpretation for observed sedimentary periodicities. Importantly, we observe the presence of obliquity-scale periodicity in sedimentation during a period of marine connection, suggesting that sea level oscillations were driven by obliquity. This observation is consistent with previous claims about the presence of a small, orbitally forced Antarctic ice sheet during the latest Cretaceous.