The overall geometry of sedimentary basins is driven by a complex interplay between subsidence, water-level variations, sedimentation rates and basin-margin topography. Seaward movement of the shoreline is driven by either high sediment input or by base-level drop. The influence of the specific driving mechanisms is often overwritten by subsequent burial and compaction effects or it is below the resolution of observational data. Our main aim is to describe and discuss the influence of these internal and external forcing factors and demonstrate their sedimentary response, particularly the related unconformities and clinoform geometries in a deep lacustrine setting. To this aim, 3D numerical simulations were performed using DionisosFlow stratigraphic forward modeling software. Models are constrained by seismic and well data from the Drava Basin part of the SW Pannonian Basin, Central Europe. A wide range of parameters, such as subsidence rates, lake-level curves and sedimentation rates were compared and analyzed. Post-rift subsidence and inversion of the basin have been simulated together with the main sedimentary transport routes. Our calculation infers that paleo-water depth could have reached ca. 1300 m in the deepest parts of the basin. Furthermore, our models show that differential compaction, subsidence and lateral variations of the sediment supply result in apparently descending shelf-edge trajectories and onlapping clinoform surfaces that are often misinterpreted as base-level drops. By analyzing the sedimentary response to different climatic variations, we argue that there is no direct indication of a major base-level drop in the Drava Basin, which was much larger than the seismic resolution, i.e. 40–50 m. Modeling also infers that autoretreat and autocyclic variations are more effective at low sediment supply and higher amplitude lake-level variations. •Forced and normal regression in analyzed in 3D models.•Kilometer-scale palaeo-water depth variations in Lake Pannon.•Tectonic motions and differential compaction overwrite clinoform geometries.•Lateral variability of sediment input rates creates pronounced unconformities.•Higher frequency climatic variations enhance the effect of autocyclic processes.