Abstract: Aquaculture is an important way for humans to obtain food, and aquaculture ponds are a major production mode of aquaculture. The Pearl River Delta, as an important aquaculture base in southern China, has undergone great changes in its spatial distribution in the past 30 years. This study investigated Zhongshan City and its adjacent areas. First, the mixed pixels of Landsat and Sentinel-2 remote sensing data were decomposed using the linear mixed pixel decomposition method. Then, the NDWI threshold range corresponding to the water abundance of 70% and above was selected through visual comparison and analysis. Finally, the spatio-temporal distribution of typical aquaculture ponds from 1990 to 2021 was obtained. The study results show that the aquaculture ponds in Zhongshan City and its adjacent areas have experienced a process of first increasing and then decreasing since 1990. Specifically, the area of aquaculture ponds nearly doubled from 1990 to 2000, tended to be stable from 2000 to 2010, but decreased by nearly 50% from 2010 to 2021. This study can reduce the impact of mixed pixels on the monitoring of aquaculture ponds and support the scientific aquaculture and sustainable development of fisheries in the Greater Bay Area.