Abstract: The change of lake water area demonstrates the impact of climate and human activities on the structure and function of the lake ecosystem, which therefore becomes an important ecological indicator for lake health assessment and water restoration. The characteristics of natural water area change under the impact of aquaculture and climate change in the past 30 years in Gaoyou Lake (including Shaobo Lake), a typical shallow lake in East China, as well as various influencing factors were analyzed. Using GIS technology, images of the Landsat TM/ETM+ remote sensing from 1988 to 2015 were set up as the data source. The boundary information of Gaoyou Lake (including Shaobo Lake) and its breeding area was extracted by visual interpretation and ratio threshold methods. The results showed that:(1) In the past 30 years, the natural water area of Gaoyou Lake tended to progressively reduce in the early stage and partially recovered in the following years:the largest area appeared was 716 km² in 1988, the smallest area was 535 km² in 2011, and 643 km² in 2015. From 1988 to 2000, the average natural water area decreased by 4.08 km²/a, whereas from 2000 to 2011 the average decrease rate was 12 km²/a, yet from 2011 to 2015 it increased by 108 km². (2) From 1988 to 2015, the annual amount of precipitation in the catchment decreased first and then increased. The annual average temperature increased gradually in relation to the change of natural water area in Gaoyou Lake (R²=0.472); There was no significant correlation between precipitation and the change of water area (R²=0.118). (3) The enclosed aquaculture lake area was neglectable before 2000, which was only 45 km² in 2000, while the largest area of 199 km² appeared in 2011. The average growth rate of aquaculture area was 15.56 km²/a from 2000 to 2009 and 9.00 km²/a from 2009 to 2015. The aquaculture was concentrated in the northern lake area, where the natural water area consequently shrank most significantly, followed by the eastern and the western lake. Since 1988, temperature and fishery aquaculture have a significant impact on the natural waters of Gaoyou Lake that the shoal in the northern part of the lake has been heavily invaded, and the ecological barrier function of wetlands has greatly declined.