Deciphering the facies and architecture of alluvial successions provides invaluable insights into the interplay of tectonics, climate, eustasy, and autogenic processes affecting terrestrial sedimentary systems. The stratigraphic response of fluvial systems to variations in discharge and sediment-supply regimes is now well-understood and is tied to changes in climate, precipitation patterns, or sediment sources. The uraniferous Chu-Sarysu Basin in south Kazakhstan occupies the tectonically stable Turan Platform on the eastern margin of the Peri-Tethys, and the study of its Palaeocene–Eocene sedimentary fill offers an opportunity to unravel eustatic and climatic controls that drove the architecture of reservoirs hosting economically important deposits. The stratigraphic succession comprises two multistorey, laterally extensive, sheet-like sandstone bodies floored by prominent erosion surfaces and interpreted as the deposits of channel belts. These packages are interstratified with floodplain, coastal-wetland, and marine-embayment complexes reflecting major extra-channel belt avulsions and marginal-marine incursions on the low-gradient alluvial plain. The stratal architecture was controlled by changes in accommodation likely induced by well-documented sea-level changes in the Peri-Tethys during the Palaeogene, which permitted the development of a chronostratigraphic framework. Eustatic variations culminated in the widespread flooding of the Turan Platform in the middle Eocene, reflected by transgressive lags above a wave ravinement surface capping terrestrial and marginal-marine deposits. Marked changes in fluvial facies, floodplain styles, and inferred channel planforms between Palaeocene and Eocene strata suggest a climatic overprint on river discharge and sedimentation. Upper Palaeocene meandering channel deposits encased in well-drained floodplain strata are indicative of perennial discharge under a semi-arid climate, whereas lower Eocene low-sinuosity channel fills, displaying evidence for transcritical flows and abundant in-situ vegetation, point to intermittent runoff patterns consistent with a humid and seasonal climate. An evolution in atmospheric moisture at the Palaeocene–Eocene boundary from arid to humid conditions has been reported across the Tethys region, and linked to global climatic perturbations of the Palaeocene–Eocene Thermal Maximum.