Seal quality assessment is not only essential in petroleum systems studies but also in the context of other geo energy applications such as underground hydrogen storage. Capillary breakthrough pressure controls top seal capacity in the absence of faults or other discontinuities. In basins that lack measured capillary pressure data (e.g., from drill cores), regional compaction-porosity trends can be used as a first prediction tool to estimate the capillary properties of mudstones. Mathematical compaction models exist but need to be calibrated for each basin. This study aims to establish a compaction trend based on theoretical models, then compare it with theoretical maximum hydrocarbon column heights inferred from true measured capillary pressure curves. Middle to upper Miocene mudstone core samples from the Vienna Basin, covering a broad depth interval from 700 to 3400 m, were investigated by X-ray diffractometry, with an Eltra C/S analyzer, and by Rock–Eval pyrolysis for bulk mineralogy, total organic carbon, and free hydrocarbon contents. Broad ion beam—scanning electron microscopy, mercury intrusion capillary porosimetry, and helium pycnometry were applied to obtain pore structural properties to compare the mathematical compaction models with actual porosity data from the Vienna Basin. Clear decreasing porosity depth trends imply that mechanical compaction was rather uniform in the central Vienna Basin. Comparing the Vienna Basin trend to global mudstone compaction trends, regional uplift causing erosion of up to ~ 500 m upper Miocene strata is inferred. A trend of increasing Rock–Eval parameters S1 and production index [PI = S1/(S1 + S2)] with decreasing capillary sealing capacity of the investigated mudstones possibly indicates vertical hydrocarbon migration through the low-permeable mudstone horizons. This observation must be considered in future top-seal studies for secondary storage applications in the Vienna Basin.