ABSTRACT Direct investigations of the connection between groundwater flow systems across multiple scales and groundwater‐dependent ecosystems (GDEs) remain rare. Such studies offer valuable insights into the complex and scale‐dependent relationships between groundwater dynamics and vegetation patterns. Our research in the Danube‐Tisza Interfluve (DTI)—an area where the preservation of natural vegetation is of critical importance—demonstrates the effectiveness of this approach in revealing the hydraulic drivers behind the distribution of GDEs. In the area, the spatial distribution of groundwater‐dependent vegetation is primarily governed by the characteristics of subsurface groundwater flow systems. Our results reveal that the chemical differences between the two dominant basin‐scale flow domains—overpressure‐related saline ascending system and topography‐driven freshwater system—are responsible for the regional distribution of habitats with alkaline and fen characteristics. Local alkaline vegetation anomalies in the fen vegetation zone are predominantly associated with the discharge zones of intermediate and local flow systems of the topography‐driven freshwater domain. Their anomalous chemical character is developed by local rock–water interactions along the local flow paths and/or by the sporadic ascent of deep saline groundwater via faults. At a small scale, the alignment between the differing chemical compositions of groundwater (saline and freshwater) and the spatial distribution of alkaline and fen vegetation could also be identified. Small‐scale investigations demonstrated that deep ascending saline groundwater associated with alkaline habitats continues to maintain them; meanwhile, habitats formed by topography‐driven flow systems are transforming, possibly because of the decreasing water supply. With this study, we highlight the critical importance of multiscale groundwater flow systems in understanding and protecting transforming GDEs—an issue that is particularly relevant in the era of climate change.