The causes of damage observed in archeological records or preserved monuments are often difficult to be determined unequivocally, particularly when the possibility of secondary earthquake damage exists. Such secondary damage has been previously proposed for the Roman Praetorium, the governor's palace in the center of Cologne. Ongoing excavations since 2007 revealed additional damage. The existing ground that has been uncovered and documented extends the affected area to 175×180 m. We present a comprehensive virtual model of the excavation area based on 200 3D laserscans together with a systematic analysis of the damage patterns and an improved model of the terrain during Roman/Medieval times including geotechnical parameters of the subsurface. Five locations with different damage patterns, including a Roman sewer, the octagonal central part of the Praetorium, a section with strongly inclined massive walls, a 13 m deep deformed well, a collapsed hypocaust, and damages in the Medieval mikveh are analyzed in detail. We use site-specific synthetic strong ground motion seismograms to test the possibility of earthquake-induced ground failures as a cause for the observed damage. This subsurface model is also used to test the possibility of hydraulically-induced damages by seepage and erosion of fine-grained material from stray sand. Heavy rainstorms can induce a direct stream of surface water through the fine sand layers to the ground water table. Simulated ground motion for assumed worst-case earthquake scenarios do not provoke slope instability at the level necessary to explain the structural damages.