This work considers the spatial distribution and ages of western MOZ basin siliclastic sediments prior to providing insights into the diagenesis of degraded dune and alluvial fan sands. Previously published and new TL/OSL ages imply that extensive over-washing of dune sands took place at least 100 ka ago while ages on Okavango floodplains imply that the fan was formed ca. 40 ka and has since undergone periods of higher and lower flood regimes. Sediment analyses indicate that both dune and fan sands contain a diagenetic matrix of clay-enhanced amorphous silica (CEAS) which bonds weakly formed aggregates. The time of formation of diagenetic matrix products is inconclusive but may have been accelerated during or shortly after events dated using OSL/TL techniques. Hence earlier dune over-washing may have led to greater porewater of an acidic to near neutral nature which in turn promoted smectite formation and silicic acid precipitation > 100 000 years ago. The relatively abundant CEAS matrix in floodplain sands implies more recent semi-continuous flood events again of an acidic-near neutral nature leading to the formation of smectite. In this case the floodplain sediments are dated as having been deposited around 40 and 11 ka, when porewater content may have accelerated clay formation and silica dissolution. The dual nature of the CEAS in the islands reflects a changing environment from smectite-dominated flooding events to sepiolite-dominated desiccation events. Flooding may also correspond to TL/OSL ages over the past 40 000 years which contributed to accelerated CEAS formation. The sepiolite is associated with a Ca-rich matrix implying desiccation which may relate to drying events over the 40 000 year period or to riparian tree root pumping and selective salt accumulation. This work shows that sedimentation in incipient rifts is complex and rarely explained totally in terms of primary depositional events. The implications of different stages of sand diagenesis may be significant in enhancing palaeo-environmental interpretations in semi-arid fluvial environments.