Our integrated tectonic and geomechanical study, based on industry-sourced data from the lower Paleozoic shale succession in the Polish part of the Baltic Basin, targeted the stress and strain conditions in which a series of tectonic structures occurred. Structural profiling of cores and scanner images from eight exploration boreholes has revealed that joint intensity profiles, bedding-parallel veins, and slickensides have a stratigraphically controlled distribution, which correlates with the intensity of hydrocarbon generation. The main three natural fracturing episodes were interpreted on the basis of the subsidence and hydrocarbon generation models. Geomechanic criteria for fracture formation combined with the geotectonic setting and hydrocarbon generation contexts have allowed the reconstruction of stress and pore pressure evolution in the mechanically layered and anisotropic rock body. Due to the high integration of tectonic and basin modeling results, a unique period in the history of the Baltic Basin was identified, in which peak gas production and maximum overpressure met the stress direction and regime changes required for fracture system formation. We have evaluated pore overpressure building components (compaction and gas generation related) and factors controlling stress changes between fracturing episodes (lithostatic unloading, thermal and pore pressure relaxation). The formulas for the stress components related to exhumation in a vertical transverse isotropic medium have been presented. Some implications for the preservation of hydrocarbon deposits in the analyzed shales are also provided.