Abstract: Understanding the spatiotemporal differentiation characteristics and formation mechanisms of space evolution of aquatic ecology in the urban agglomerations of the middle reaches of the Yangtze River is crucial for implementing land use control and integrating aquatic ecological space governance into the territorial spatial planning system. This study constructed a classification system for aquatic ecological space, tailored to the current demands for spatial use regulation in territorial spatial planning. Using a spatial transfer matrix and topographic position analysis, the study delineated the spatiotemporal evolution of aquatic ecological space from the dual perspectives of "scale-topography." Additionally, a Partial Least Squares Structural Equation Model (PLS-SEM) was introduced to quantitatively analyze the mechanisms underlying the aquatic ecological space patterns in the study area from 2000 to 2020. The results revealed that: 1) Over the past two decades, the aquatic ecological space had diminished by 1 614.26  km2, a decrease of 7.63%, with significant reductions in Hubei and Hunan provinces, and a slight increase in Jiangxi province. The dynamic conversion between "agricultural space and aquatic ecological space" was particularly pronounced, with the most intense transitions observed in the Jianghan and Two Lakes Plains; 2) From a topographic gradient perspective, the loss and expansion of aquatic ecological space predominantly occurred in low topographic regions, with an overall trend of shifting toward higher elevations; 3) The PLS-SEM effectively elucidated the relationships between aquatic ecological space and multiple influencing factors, even with small sample sizes and non-normally distributed spatial data. The evolution of aquatic ecological space was significantly influenced by geomorphological foundations, road infrastructure development, and agricultural production activities. Population growth, social development, and economic and industrial expansion exerted indirect impacts through road infrastructure and agricultural production, while climatic and hydrological changes had a notable effect solely on the expansion of aquatic ecological space. This study provided theoretical support and data references for the quantitative analysis of the pattern-process-mechanism of aquatic ecological space under the context of territorial spatial planning in the urban agglomerations of the middle reaches of the Yangtze River.