The seawater intrusion process is characterized by the difference in freshwater and seawater density that causes freshwater to float on seawater. Many confined aquifers have a large horizontal extension with respect to thickness. In these cases, while buoyancy acts in the vertical direction, flow is confined between the upper and bottom boundaries and the effect of gravity is controlled by variations of aquifer elevation. Therefore, the effective gravity is controlled by the slope and the shape of the aquifer boundaries. Variability in the topography of the aquifer boundaries is one case where 3D analysis is necessary. In this work, density-dependent flow processes caused by 3D aquifer geometry are studied numerically and specifically, considering a lateral slope of the aquifer boundaries. Sub-horizontal circulation cells are formed in the saltwater entering the aquifer. The penetration of the saltwater can be quantified by a dimensionless buoyancy number that measures the lateral slope of the aquifer relative to freshwater flux. The penetration of the seawater intrusion wedge is controlled more by this slope than by the aquifer thickness and dispersivity. Thus, the slope must be taken into account in order to accurately evaluate seawater intrusion.