Sedimentological and palynological investigations of Great Songkhla Lakes, east coast of the Malay-Thai Peninsula, Southeast Asia, reveal sedimentary sequences rich in palynomorph assemblages dominated by pollen of mangroves and freshwater swamps. Compared with other regions in Southeast Asia the assemblages are of relatively low diversity. Geochronological data indicate that the Great Songkhla Lakes record one of the earliest mangrove environments in Southeast Asia (8420–8190 cal. yr BP), which are subsequently replaced by a freshwater swamp at 7880–7680 cal. yr BP owing to the decline of marine influence. Sea-level observations from Great Songkhla Lakes and other areas of the Malay-Thai Peninsula reveal an upward trend of Holocene relative sea level from a minimum of − 22 m at 9700–9250 cal. yr BP to a mid-Holocene high stand of 4850–4450 cal. yr BP, which equates to a rise of c. 5.5 mm/yr. The sea-level fall from the high stand is steady at c. − 1.1 mm/yr. Geophysical modelling shows that hydroisostasy contributes a significant spatial variation to the sea-level signal between some site locations (3–4 m during the mid-Holocene), indicating that it is not correct to construct a single relative sea-level history for the Malay-Thai Peninsula.