A three-dimensional (3-D) outcrop depositional facies investigation of carbonate reservoir analogues requires a comprehensive integration of outcrop with “behind-the-outcrop” geophysical data. This study proposes a comprehensive methodology to assess, process, and synthesize photogrammetry, sedimentology, ground-penetrating radar (GPR), and seismic data sets based on the outcrop depositional facies framework. The methodology was tested and applied to map the 3-D morphology of the stromatoporoid-coral buildups in the Upper Jurassic Hanifa Formation reservoir analogue at Wadi Birk, Saudi Arabia. Data sets acquired include 1.2 km2 drone imageries; measured sections; 8-km-long networks of two-dimensional (2-D) GPR, three grids of 3-D GPR (60 × 50 m; 50 × 20 m; 55 × 40 m); 640-m-long 2-D seismic profile; and a 50-m-long core. We constructed a digital outcrop model (DOM) from drone imageries and calibrated it with measured sections. We measured dielectric permittivity, acoustic velocity, and bulk density to assess the geophysical properties of the target facies. We used DOM-based GPR and seismic models to assess the geophysical responses and formulate processing flows that accentuate anomalies from the stromatoporoid-coral facies. We used the proposed methodology to measure the 3-D morphology of the stromatoporoid-coral buildups quantitatively. The buildups are 3-D pseudo-ellipsoidal with an average long and short axis length of ∼36 and ∼11 m, respectively. The average thickness of the buildups is ∼2.6 m with ∼N335E orientation. We used these statistical measurements to construct an outcrop-based porosity model of the Hanifa reservoir analogue that honors the observed 3-D morphology of the stromatoporoid-coral facies.