We studied Holocene paleolimnological changes inferred from multi-proxy data set of CNS elements, biomarkers and microscopic observation of microalgae and cyanobacteria in sediment cores from Rundvågshetta lakes (Maruwanminami-ike and Maruwan o-ike) in the Soya Coast region of East Antarctica, along with sedimentary facies and AMS 14C dating. They are discussed with paleoenvironmental changes, transition ages and glacio-isostatic uplift rates in the Soya Coast region and East Antarctica. Ages of the Maruwanminami-ike core (MwS4C-01, length 147 cm) and Maruwan-oike (Mw4C-01, length 226 cm) ranged from 1,230-5,010 cal BP) and 2,240-5,700 cal BP, respectively. Reservoir effects of the Rundvågshetta lakes were very high which may be due to the influence of dead carbon in glacially eroded marine sediments and base rocks. Average sedimentation rates of Lakes Maruwanminami-ike and Maruwan-oike were 0.389 and 0.649 mm/yr, respectively. Crustal uplift rates of Lakes Maruwanminami-ike and Maruwan-oike determined by sedimentary facies, green sulfur bacterial biomarkers and diatoms were estimated to be 8.24 and 8.25 mm/yr, respectively. Coastal marine environment: Maruwanminami-ike (147-72.5 cm, 5,010-2,590 cal BP) and Maruwan-oike (226-47.2 cm, 5,700-3,190 cal BP) were characterized by low biological production with the predominance of diatoms. Transition period of stratified brackish lake environment: Maruwanminami-ike (72.5-65.6 cm, 2,590-2,500 cal BP) and Maruwan-oike (47.2-28.8 cm, 3,190-2,890 cal BP) were characterized by stratified conditions with marine water overlain by freshwater, and a chemocline developed together with an anoxic layer in the bottom of photic zone. Freshwater lake environment of Maruwanminami-ike (65.6-0 cm, 2,500-1,230 cal BP) was characterized by high biological production by cyanobacteria (e.g. Leptolyngbya spp.) and green algae (e.g. Comarium clepsydra) with some contribution of diatoms, while that of Maruwan-oike (28.8-0 cm, 2,890-2,240 cal BP) was very low biological production. The marine to terrestrial transition ages of raised beaches and isolated basins in the Saya Coast region ranged from 970 to 9,290 yr BP with an average of 3,660±1,520 yr BP (standard deviation) suggesting that major warm periods in the region are the middle Holocene. Glacio-isostatic uplift rates of raised basins and isolated basins in the Soya Coast region ranged from 0.19 to 4.40 mm/yr with an average of 2.0 ± 0.92 mm/yr which is similar to East Antarctica. Glacio-isostatic uplift rates of raised beaches are correlated with altitudes with a correlation coefficient of r2 = 0.724. Increasing crustal uplift rates with altitudes reflect continuous crustal uplifts in the Soya Coast region.