Ancient maritime trading ports along the southern coast of Oman have been the target of archaeological excavations for several decades. Though historical chronologies are well-researched, information from a paleoenvironmental perspective is lacking and can provide a more complete understanding of site development. This study investigates the timing of coastal sand barrier accumulation in the natural harbours at Khor Al Balid and Khor Rori, which had considerable effects on the populations at the ancient cities of al–Balīd and Sumhuram, respectively. Six cores from Khor Al Balid and four cores from Khor Rori were analyzed using sedimentological, microfossil (foraminifera and testate amoebae), geochemical (μXRF), and radiocarbon dating methods. Marine proxies (e.g., Amphistegina spp., C. pseudolobatulus, E. limbatum, Sr, Ca/Si) and lagoon proxies (e.g., T. macrescens, T. inflata, C. constricta and C. aculeata, Ti/Ca, Fe/Ca) were used to identify Marine Sand, Brackish Lagoon/Marsh, and Freshwater facies. Results indicate that the eastern arm of Khor Al Balid closed off from the sea around the 12th century CE and that the western arm closed around the 15th century CE. Siltation of harbours and the formation of sand barriers may have contributed towards site abandonment. Previous archaeological findings suggest that al-Balīd was able to continue with maritime trade activities along the southern seaside edge of the city for several centuries after siltation of Khor Al Balid, possibly with the help of dredging. An extreme overwash event was recorded in almost all cores across both sampling sites, suggesting that a very large cyclone or a tsunami hit the southern Oman coast sometime around the 18th–19th century CE. This event, as well as continuous coastal sand accumulation, may have contributed to the decline and abandonment of Khor Al Balid and highlights the impacts that large storm/wave events have on archaeological site preservation.