Understanding the spatiotemporal evolution of hydro-ecological space and its eco-environmental effects within the territorial spatial system is essential for supporting the high-quality development of projects along the middle route of the South-North Water Diversion Project. Using annual land-use data from 2000 to 2023, this study combined space-time cube analysis, an eco-environmental quality index, and interpretable machine learning to investigate the spatiotemporal evolution patterns, eco-environmental effects, and driving mechanisms of hydro-ecological space along the middle route. The results indicated that:(1) Hydro-ecological space exhibited a fluctuating expansion of 162.02 km² over 2000-2023, increasing its share of total territorial space to 1.56%. The evolution pattern exhibited strong spatial differentiation: it expanded in the water source and water receiving areas but declined markedly in the downstream section. As the study period extended, the regional distribution becomes increasingly polarized between water-abundant and water-deficient areas. (2) Land-use conversions involving hydro-ecological space totaled 5555.06 km², accounting for 9.62% of all territorial spatial structural changes. Conversions between hydro-ecological space and agricultural space dominated (61.65%). Structural transformations of hydro-ecological space improved overall regional eco-environmental quality, but after the middle route of the South-North Water Diversion Project was put into operation for water transfer, the downstream section experienced a marked decline in eco-environmental quality. (3) The evolution mechanism was characterized by policy and engineering guidance, constraints from natural geographical conditions, impetus from transport infrastructure development, and responses to socio-economic development, with driving factors exhibiting complex interactions and nonlinear effects.