In arid inland watersheds, the compounding impacts of climate change and intensive human activities have severely altered hydrological regimes and accelerated landscape degradation. However, conventional spatial planning often overlooks the critical coupling between subsurface hydrological processes and surface landscape dynamics. Taking the Manas River Watershed in northwestern China as a representative case, this research investigates the multi-scale dynamics of landscape patterns and their underlying spatial determinants. Integrating multi-period land-use data (2000–2020), landscape metrics, and the GeoDetector model, we diverge from conventional uniform buffer approaches by redefining riparian boundaries utilizing four distinct River–Groundwater Transformation (RGT) patterns. This methodological shift reveals critical eco-hydrological heterogeneities previously masked by fixed-width approaches. Our multi-scale analyses demonstrate that watershed-level landscapes exhibited a trajectory of declining diversity, transient recovery, and ultimately, intensified fragmentation, while riparian patches concurrently expanded and became increasingly homogenized. GeoDetector assessments indicate a fundamental shift in driving forces: early-stage variations were constrained by natural factors, whereas post-2010 dynamics became overwhelmingly dominated by socio-economic determinants, particularly agricultural expansion and GDP growth. Crucially, our RGT-coupled spatial analysis reveals a strong spatial association between agricultural sprawl and landscape risk hotspots concentrated within groundwater overflow zones—a pattern consistent with, but not directly demonstrating, disrupted vertical hydrological connectivity. Direct verification of subsurface mechanisms would require continuous piezometric monitoring beyond the scope of this study. Consequently, rather than generic zoning, we propose a multi-scale “hydro-spatial” governance framework featuring targeted interventions. By establishing strict agricultural redlines in vulnerable overflow zones and implementing eco-hydrological restoration tailored to specific RGT regimes, this paradigm delivers robust methodological insights for advancing precision spatial planning in fragile arid ecosystems.