Vegetation on dunes regulates the water supply from the dunes to the inter-dune lowland, which is a crucial factor affecting lake water dynamics in the inter-dune lowland. Previous researchers have paid insufficient attention to the water regulation function of dunes on a landscape- and regional scale. To fill this gap, both remote sensing technology and field observations were used to analyze the variations in the lake area and their influence factors, such as vegetation coverage and precipitation in the lake watershed, on a multi-year scale (2000–2020) and one-year scale (2021), respectively. The results showed that precipitation is the main factor influencing the changes in lake water, and artificial sand vegetation can regulate the changes in lake water. On the multi-year scale, with the coverage of artificial sand-fixing vegetation increasing on sand dunes in the lake watershed, the areas of the lakes were gradually decreasing. On the one-year scale, with dune vegetation coverage increased, the water supply from dunes to lakes showed a decreasing trend. This model can provide a possibility for estimating and predicting the influence of water supply from dunes to lakes that is affected by sand-fixing vegetation. The findings have significant theoretical and practical utility for the rational utilization of water resources in sandy land, as well as for assisting in the selection of an optimized construction mode for desert control projects.