Whereas conductive geothermal models of oil formation have been used by geologists for more than two decades, the effects of convective heat transfer as an agent in petroleum genesis have only recently been proposed. In this paper, mathematical modeling is used as a tool to gain insight into the impact of groundwater flow on petroleum generation within one important class of sedimentary basins: continental rift systems. One-dimensional and two-dimensional finite element models are presented that illustrate the importance of convective heat transfer for geochemical models of petroleum generation at different levels of complexity. The simple one-dimensional models of hydrothermal fluid flow and petroleum generation constructed for idealized groundwater recharge and discharg areas within subsiding rifts indicate that vertical groundwater flow rates on the order of 1 mm/yr cause a shift in the depth to and width of the oil window by hundreds of meters. The effects of transient hydrothermal fluid flow on maturation indices were found to be preferentially preserved in groundwater discharge areas. A two-dimensional field application of the model to the Rhine graben indicates that, following marine regression at 15 Ma, a regional topography-driven groundwater flow system was established that shifted the depth to the oil window between recharge and discharge areas by more than 1 km. These findings are supported by present-day heat flow and thermal maturation data collected within the rift.