This study investigated Holocene paleolimnological changes inferred from a multi-proxy dataset of C, N, and S elements, biomarkers, and microscopic observations of microalgae and cyanobacteria in sediment cores from two Rundvågshetta lakes (Maruwanminami-ike and Maruwan-oike) in the Soya Coast region of Antarctica, along with sedimentary facies and accelerator mass spectrometry 14C dating. We discuss biological production and sources, the transition from marine to brackish and lacustrine environments in the lakes, paleoenvironmental changes, transition ages, and relative sea level (RSL) falls (or subsidence) from glacial isostatic adjustment (GIA) in the Soya Coast region. The ages of the Maruwanminami-ike (MwS4C-01, length 147 cm) and Maruwan-oike sediment cores (Mw4C-01, length 226 cm) were 1.4 (5.8 cm core depth)–4.9 and 2.3–5.7 cal ker BP, respectively. The local reservoir effects of the Rundvågshetta lakes were very high, possibly because of the influence of dead carbon in the glacially eroded marine sediments and bed rock. The coastal marine environments of Lakes Maruwanminami-ike (4.9–2.6 cal ker BP) and Maruwan-oike (5.7–3.3 cal ker BP) were characterized by low biological production. A transition period marked by a stratified brackish lake environment in Lakes Maruwanminami-ike (2.6–2.4 cal ker BP) and Maruwan-oike (3.3–2.9 cal ker BP) was characterized by stratified conditions with an anoxic layer at the bottom of the photic zone. The freshwater lake environment of Lake Maruwanminami-ike [(65.6–0 cm, 2.4–1.4 (5.8 cm core depth) cal kyr BP)] was characterized by high biological (cyanobacteria and green algae) production, while that of Lake Maruwan-oike (2.9–2.3 cal ker BP) was characterized by low biological production due to the influence of glacial clay. Around 7.2–3.0 cal ka BP in the Holocene was probably a warm period, and progressive glacial retreat with RSL fall occurred during the warm periods in the Soya Coast region. The RSL falls of all raised beaches and isolated basins in the Soya Coast region ranged from 0.36 ± 0.03–4.4 ± 0.5 mm/yr with an average 2.1 ± 0.2 mm/yr (standard deviation, SD). They were similar to GNSS–based GIA–induced uplift with an average of 2.4 ± 1.5 mm/yr (SD) at Soya Coast region.