The mid-Holocene sea-level highstand is a well-known phenomenon in sea-level science, yet the knowledge on the highstand’s spatial and temporal distribution remains incomplete. Here we study the southwest coast of the Arabian-Persian Gulf where a mid-Holocene sea-level highstand and subsequent sea-level fall may have occurred due to the Earth crustal response to meltwater load. Sea-level indicators were established using standard facies analysis and error calculations, then constrained through glacio-isostatic adjustment (GIA) modelling and though procedures based on Gaussian Process and exponential decay analysis. This work allowed to identify the highstand at 1.6 ± 0.4 m occurring 6.7–6.0 ka, in excellent agreement with GIA model results. The subsequent shoreline migration followed the geophysical constraint by prograding in line with the sea-level fall until around 3 ka. Then, the strength of the external control weakened and internal processes, in particular sediment binding through microbial activity, started controlling the geometry of the accommodation space.