Meltwater drainage through glaciers strongly influences ice dynamics and related hazards, yet detailed observations of active englacial and subglacial networks remain scarce due to challenges in direct observation. We present a novel high-density, UAV-based 3D ground-penetrating radar (GPR) survey of Switzerland’s Otemma Glacier, integrated with dye tracing experiments, photogrammetry and hydraulic potential modeling, to map internal water pathways with unprecedented spatial resolution and coverage. Advanced 3D imaging techniques, adapted from seismic diffraction processing, enhance the detection of small-scale conduits within the ice. We identify two primary subglacial channels having distinct hydraulic efficiencies and transport behaviors. Englacial drainage is found to be structurally complex, comprising lateral conduits, branching networks and localized pooling zones. These observations provide critical constraints on the geometry and dynamics of glacier drainage, supporting and extending existing models, and are essential for forecasting glacier behavior under future warming. UAV-based 3D GPR, in combination with novel processing strategies, emerges as an innovative approach for large-scale, repeatable surveys of glacier hydrology.