The Taiwan coastal areas are facing predicted sea-level rise effects in the global climate change context. Better understanding of the mechanisms and forcing factors driving the geomorphological evolution of Taiwan’s coastline is essential. We highlight the potential of small river estuaries as archives of coastal evolution and provide a paleo-environmental reconstruction of the Gangkou River estuary based on results from a combined methodological approach using geomorphological, sedimentological, and geochronological analyses. A consistent chronology was established by combining Optically Stimulated Luminescence (OSL) dating, as well as radiocarbon dating techniques. A distinct beach-rock layer allowed firm correlation of six investigated coastal profiles. Eustatic sea level change was identified as the primary coastal and estuarine landscape development forcing factor in the study area. Tectonic forcing could also be detected from the investigated sites, but has to be regarded as a subordinate secondary forcing factor. The Gangkou River estuary developed in the early Holocene at about 8 ka and was fully developed by the time the Holocene sea-level maximum was reached. With the sea-level dropping until modern times, estuarine zone relocation and a transition to terrestrial processes was initiated, leading to development of the current coastal dune system since about 2.5 ka. Major dune building phases correlate with the climate change associated with the Little Ice Age (LIA) event and stabilised towards recent times, which is in accordance with regional and over-regional coastal Aeolian records in Taiwan.