The South African coast contains abundant estuaries and lagoons, most of which originated as river valleys incised during Quaternary sea-level fall and subsequently drowned and/or infilled during rising interglacial sea levels. This chapter discusses these changes and highlights the geomorphological and sedimentological evolution of several southern African estuaries during the Pleistocene to present. The development, infilling and positioning of incised valley systems is mainly controlled by sea-level variation as well as fluvial and marine sediment supply. Most contemporary estuaries in southern Africa show dramatic responses to shorter term sea-level fluctuations and sediment supply during the Holocene. Barring anthropogenic interference, the dynamic behaviour of estuaries, dictated by their transient position and geomorphic character within an incised valley, is considered to fluctuate on centennial to millennial timescales.