Both shallow and deep groundwater flow mediates a variety of geologic processes. In the discharge zones of the nested groundwater flow systems, saltwater often emerges due to high evaporation (in endorheic drainage basin), tide surge, or marine transgression and regression (in coastal areas) or salt pollution (in streams). However, to our best knowledge there are limited studies that consider the impact of density flow in the discharge zone on the nested groundwater flow systems. In this study, nested groundwater flow systems are analyzed with saltwater infiltration in their discharge zones. To quantify the effects of saltwater concentration on the flow systems, seven scenarios with different saltwater concentrations in the discharge zones are modeled. It is found that the flow systems are most sensitive to the saltwater concentration of the discharge zones when the concentration is between 2.23 and 4 g/L, and the threshold saltwater concentration that starts to affect the flow systems is about 1.35 to 2.23 g/L for the specific aquifer configuration selected for this study. The results also show that the local flow systems retreat upward and the overall groundwater velocity of the entire flow systems is decreased with the increase of the saltwater concentration. This study may shed light on the control of salinization, evolution of saline lake basins, and seawater intrusion from a perspective of nested groundwater flow systems.