Hwajinpo is the largest lagoon in Korea and is located along the east coast of the country. It possesses Holocene sediments that provide an important record of past climate change. We studied the evolution of Hwajinpo Lagoon using grain size data and diatom assemblages in an 11.0-m core (HJ02), which was obtained at the mouth of a small river that drains into the lagoon. Core chronology was established with accelerator mass spectrometry 14C dates and optically stimulated luminescence dates. Diatom assemblages and grain size analysis revealed that estuarine conditions in the inner lagoon area transitioned to an open embayment ca. 8 ka as a result of sea-level rise. Around 7.8 ka, the open bay became a semi-closed bay as a consequence of development of a sand barrier. After the bay was semi-closed, marine water inflow was increasingly restricted as the sand barrier developed, and the semi-closed bay became a completely enclosed, low-salinity, brackish lagoon around 6 ka. There was an erosional hiatus between 5.5 and 1.7 ka (7.0 m depth), likely caused by river flooding and a switch in the location of drainage along the delta. The lagoon became oligohaline around 1.6 ka, likely because of increasing precipitation associated with an intensified Asian summer monsoon. This increase in precipitation resulted in expansion of the sand bar by sediment inflow, driven by agricultural development in the area. About 1000 years ago, the diatom assemblage was similar to the modern assemblage, suggesting the lagoon’s current geomorphic conditions had been established.