In this work, we extend a planar laser-induced fluorescence method for free surface measurements to a three-dimensional domain using a stereo-camera system, a scanning light sheet, and a modified self-calibration procedure. The stereo-camera set-up enables a versatile measurement domain with self-calibration, improved accuracy, and redundancy (e.g., possibility to overcome occlusions). Fluid properties are not significantly altered by the fluorescent dye, which results in a non-intrusive measurement technique. The technique is validated by determining the free surface of a hydraulic flow over an obstacle and circular waves generated after droplet impact. Free surface waves can be accurately determined over a height of L= 100 mm in a large two-dimensional domain (y(x, z) = 120 × 62 mm2), with sufficient accuracy to determine small amplitude variations (η≈ 0.2 mm). The temporal resolution (Δt= 19 ms) is only limited by the available scanning equipment (f= 1 kHz rate). For other applications, this domain can be scaled as needed. Graphic abstract: [Figure not available: see fulltext.].