Poyang Lake, the largest freshwater lake in China, plays a critical role in regional water security and the integrity of wetland ecosystems. Seasonal isolated lakes(SILs), as important components of the Poyang Lake wetland system, exhibit dynamic changes in water level and volume that directly affect the lake’s water balance and biodiversity conservation. However, due to limited in situ observations, complex land surface conditions, and frequent wet–dry alternations, existing methods for estimating water volume suffer from limitations in both accuracy and applicability. This study proposes a novel method for estimating the water volume of SILs by integrating multi-source remote sensing data, hydrological connectivity analysis, digital elevation models (DEMs), and limited hydrological measurements. For the first time, high-resolution time series (8-day, 30-meter) data on water surface area, water level, and water volume were reconstructed for 102 SILs from 2000 to 2024. Results show that: (1) the timing of isolated phases varies spatially, with average Xingzi Station water levels of 13.85 m and 14.28 m marking the start and end of isolation in the Ganjiang North tributary; (2) the 102 SILs had an average area of 305.20 km2, accounting for 17.98% of Poyang Lake’s surface water area, with the largest isolated area recorded in 2023 (134.03 km2, 8.29% of the lake’s area that year); (3) during the rising, falling, and dry water stages, the water volume of SILs accounted for 1.91%, 4.13%, and 6% of the total lake volume, respectively. From 2000 to 2024, water volume in northern lakes showed a declining trend, while lakes in the central and southern regions showed increasing trends, playing a positive role in mitigating drought stress in the basin. Overall, this study offers a new technical pathway for hydrological monitoring and management of Poyang Lake and other small, shallow, seasonal lakes, providing a scientific foundation for sustainable water resource use and ecological protection.