The late middle Miocene Quebrada Honda Basin of southern Bolivia has long been studied for its diverse fossils of terrestrial vertebrates and, more recently, for its record of paleoelevation and paleoclimate in the Eastern Cordillera of the Andes Mountains. This paleobiological and paleoenvironmental archive is constrained by high resolution radioisotopic ages linked to paleomagnetic reversal stratigraphy in multiple areas within the basin. Nevertheless, studies of the basin's stratigraphy have been limited and questions remain about how the sedimentary deposits and fossil horizons in different parts of the basin relate to each other. We confirm the identification of three lithostratigraphic units, show that the units extend across the basin, and examine the distribution of sedimentary and pedogenic facies and volcanic tuffs within them. We identify different styles and stages of pedogenic development that correspond to mappable differences in outcrop character. Volcanic tuffs and sedimentary and pedogenic facies exhibit high lateral continuity consistent with accumulation on a low relief basin floor. In contrast, sedimentary and pedogenic features change vertically over multiple scales reflecting secular variations in aridity and stability over seasonal to multimillennial scales. Erosional truncation of lithostratigraphic units and a ~ 700,000-year gap in the ages of superimposed strata delineate an erosional unconformity with >50 m of relief that was cut ~12 million years ago. Breach of the basin margin along a boundary between local structural blocks may account for the development of localized incision during a period when landscapes of the Eastern Cordillera were stable with little deformation or erosion. Regional landscape stability at that time has been attributed to low elevation or a position behind an orographic precipitation barrier. The sedimentary and pedogenic facies, faunal communities, and intraformational unconformity of the Quebrada Honda Basin favor a low elevation setting, which has implications for the timing and mechanisms of uplift of the Bolivian Andes.