This paper focus on the Holocene palaeogeography of the Ja'alan coast from the 6th to the 4th millennium cal. BC, integrating the dynamics of mangroves, lagoons, khors-estuaries and deltas, with sea-level change and the evidence from Neolithic shell middens. The distribution and maturation of mangrove ecosystems along the Arabian coasts has varied considerably, affected by physical forces such as sea-level changes, climate, tidal amplitude and duration as well as the quantity of fresh water inflow associated with the monsoon systems along the Arabian coast. Palaeo-mangroves and lagoons, today replaced by large sabkhas, appear to be correlated to mid-Holocene fossil deltas and estuaries that currently function episodically, depending on the rhythm of winter rains. All these parameters have determined and impacted the location of settlement networks and the economic strategies of the first Arabian farmers along the eastern Arabian coast. The mid-Holocene sea-level highstand stability (5th millennium BC) can be considered to be an optimum period for mangrove development and can be correlated with Neolithic sites around the mangroves. The decline of mangroves since 3000/2500 cal. BC and further degradation is mainly attributed to the prevailing arid climate that reduced summer monsoon effects in the tropical area by favouring the extension of sabkhas. We discuss these aspects based on new archaeological surveys, excavations and geoarchaeological studies.