Secondary migration is the process by which petroleum is transported from the pod of active source rock to the trap. Most petroleum migrates as a separate, immiscible phase through water-saturated rock. The driving force for migration is the vertical buoyancy force due to the lower density of petroleum compared to that of formation water. The capillary pressure difference between the oil and water phases opposes the buoyancy force, discouraging the entry of petroleum into smaller water-wet pores. The interaction of these two forces causes petroleum to migrate along coarser parts of the "carrier bed," often by a tortuous pathway that is disrupted by the presence of heterogeneities. Subsurface water potential gradients due to active aquifers or rapid sedimentation (such as n the Gulf Coast) can alter the direction of secondary migration. Secondary migration by aqueous solution is not expected to be a significant process due to the low solubilities of most components of petroleum.

Secondary migration efficiency is an important parameter when estimating the degree of fill of a prospect or the location of dry hole belts. It can be estimated by a statistical analysis of past exploration results or by assuming that a certain fraction of the migration pathway's pore space must be saturated by petroleum before a prospect can fill with oil or gas.

Once petroleum starts to fill a trap, the tortuous migration pathway tend to fill from one side. Because petroleum composition changes with time as the source rock becomes more mature, compositional differences (e.g., in GOR, API gravity) may be "inherited" from the filling process. In the presence of barriers, diffusional and convective mixing may be too slow, even on geologic time scales, to eliminate all compositional differences. By examining present-day compositional differences from a set of wells in a field under appraisal or development, it is possible to identify the presence of flow barriers and the direction from which the field filled.