The subsurface plumbing system of ancient seeps of hydrocarbon-rich gases and fluids is partially preserved by seep deposits in Miocene rocks of the Coast Ranges and on the seafloor of the Monterey Bay region in central California. The fossil seep-related deposits are of two types: authigenic carbonates and intrusions of oil-saturated sandstones. Both types occur in fractured and faulted siliceous mudstone and porcelanite layers of the organic-rich Miocene Santa Cruz Mudstone. They are associated with tectonic structures indicating deformation, and are located in the proximity of faults. The morphology of the seep carbonates is characterized by strong asymmetries and by holes, pipes and other types of fluid conduits with orientations parallel to the directions of the local fracture- and fault-sets, thus suggesting structural control over pathways of fluid migration. The dominant direction of the conduits in the seep carbonates and of the intrusive dikes (northeast–southwest) differs from the dominant orientation of the tectonic structures of the San Andreas Fault System (northwest–southeast). Previous interpretations of these ancient seep-related deposits suggested that lateral changes of the thickness of the Cenozoic marine host sediments favored fluid migration from basin depocenters located offshore toward basin margins. Different driving forces for fluids have been hypothesized including hydrocarbon generation, differential compaction, and tectonic compression. Most of the fossil seeps are located on structural highs of the basement and adjacent to offshore basins that form elongated depressions oriented northwest–southeast. Previously unidentified structures that offset the basement along northeast–southwest trends (cross-setting faults) paralleling the orientations of the conduits of the seep carbonates and the dikes of oil-saturated sandstones were also recognized. Tectonic deformation, block rotations (documented by local clockwise rotations of paleomagnetic directions in the Coastal Ranges) and cross-faults were probably produced during the Late Miocene and Pliocene to accommodate the shear stress between conjugate faults during eastward shifting of the activity of the San Andreas Fault System. Comparison with previous studies on ancient seep deposits, regional geology and offshore tectonic data, suggest that the fluids that sourced the seeps were driven by episodes of inverse tectonics, during which previously extensional depositional basins were involved in episodes of tectonic compression. Tectonic deformation created cross-faults in rotated blocks, which could have acted as important conduits for the flow of hydrocarbon-rich fluids and gases and fostered the injection of liquefied sands.