This study examines both the inlet dynamics, recorded in the back-barrier stratigraphy of Kosi Bay, and the competing effects of waterbody segmentation on along-strike changes in the character and nature of an incised valley fill at Kosi Bay, South Africa. The Kosi Bay system comprises four interconnected lakes (Lake Makhawulani, Lake Mpungwini, Lake Nhlange and Lake Amanzimnyama) subject to varying degrees of marine influence. Formerly, the system's only connection to the ocean was through the Bhanga Nek palaeo-inlet. The location of this system behind a continuous coastal barrier predisposes it to excellent archives of environmental change related to changing sea-level and sediment supply. In this context, two cores were extracted from the system (KB2 and KB4), together with over 150 km of seismic reflection profiling, as well as AMS radiocarbon analyses and legacy data in order to present a new stratigraphic evolution model for this back-barrier system. A total of 5 seismic units were imaged (Units A-E). A major unconformity surface (SB), characterised by broad u-shaped incised valleys, incises the underlying unconsolidated sandy acoustic basement (Unit A). Unit B forms as thickly developed central basin deposits, partially infilling the incised valleys. Two forms of prograding spits are evident ̶Unit C1 progrades from the palaeo-highs of the valley interfluves into the nearest available accommodation space and Unit C2 progrades from the margins of the system into the basin. These are separated by an erosional surface (T-RS) formed by migrating tidal channels as sea-level rose and marine waters entered the system during the Holocene. Unit C2 spits are in turn associated with slump deposits formed on the steepest part of the margins (Unit D) that were dated to 2900 ± 165 cal. BP. The unusual depth of Surface T-RS is attributed to (1) limited sediment supply during sea-level rise, (2) the presence of easily erodible fine sediments in which this surface erodes and (3) a larger tidal prism when the Bhanga Nek inlet was still open and system segmentation by Units C2 and D had not yet occurred. Unit E caps the stratigraphy and is interpreted as lacustrine fines with a thin layer of acoustically transparent material (gyttja) on top. The deposition of Unit E signifies the closure of the system to the ocean and the overall shift from an estuarine/lagoon environment to a lacustrine one. Recalibrated AMS dates place the system closure to between 3160 and 2900 cal. BP, coeval with the formation of the prograding marginal spits and waterbody segmentation (Unit C2). Along-strike variation in the timing of the basin infilling, attributed to changes to the inlet functioning coupled to the segmentation of the waterbody, is characteristic of this area. At 1450 cal. BP, a new tidal inlet formed to the north of Lake Makhawulani, where impounded waters were diverted via a low point in the back-barrier coastal dune cordon. The formation of this inlet suggests a prolonged period of back-barrier flooding until a low point in the barrier was breached during the Holocene sea-level highstand of 1.5 m. Such inlet development and along-strike back flooding of incised valleys is an unusual attribute of coastal waterbodies of South Africa.