ABSTRACT The ephemeral braided Hoanib River of NW Namibia flows for a few days a year, and only high discharges enable the river to pass through interdunal depressions within the northern Namib Desert dune field to the Atlantic. The dune field comprises mainly large transverse dunes resulting from predominant SSW winds. River flood deposits between aeolian dunes are analogous to mudstone layers conformably interbedded with ancient aeolianite dune foresets. Deep floods pond laterally to considerable depths (metres to >10 m) in adjacent interdunes, depositing mud layers (1–50 cm) to considerable heights on avalanche and stoss faces of bounding dunes. Fairly passive flooding only disturbs aeolian stratification minimally. Floodwater clay infiltrates and settles as an impermeable seal, with a flood pond on top, perched, above regional groundwater. Flood ponds evaporate slowly for long periods (>3 years). Early emergence desiccates higher parts of a mud layer. Subsequent floods can refill a predecessor pond, benefiting from the existing impervious seal. Potential preservation of such mud layers is lower on the stoss face, but high on the avalanche face after burial by subsequent dune reactivation and migration. The leeward (right) Hoanib bank, a dune stoss face, is river and wind eroded to exhume fossil interdune pond mud layers of an earlier Hoanib channel. The highly inclined layers are interbedded with dune avalanche foresets and represent the edges of two successive fossil ponds exposed in plan. Ancient flood pond mudstones occur in the Permian–Triassic hydrocarbon reservoir, the Sherwood Sandstone Group of the Cheshire Basin (Kinnerton Formation) and Irish Sea Basin and were previously used erroneously to argue against the aeolian origin of cross-bed sets. Hoanib studies show that primary river interaction with a dune field might preserve only localized erosional omission surfaces in ancient aeolianites, with little sandy barform preservation, prone to aeolian reworking. Around the main fluvial channel locus, however, flood pond mudstone layers should form a predictable halo, within which fluid permeability will decrease.