Physical barrier has been proven to be one of the most effective measures to prevent and control seawater intrusion (SWI) in coastal areas. Mixed physical barrier (MPB), a new type of physical barrier, has been shown to have higher efficiency in SWI control. As with conventional subsurface dam and cutoff wall, the construction of MPB may lead to the accumulation of nitrate contaminants in coastal aquifers. We investigated the SWI control capacity and nitrate accumulation in the MPB using a numerical model of variable density flow coupling with reactive transport, and performed sensitivity analysis on the subsurface dam height, cutoff wall depth and opening spacing in the MPB. The differences in SWI control and nitrate accumulation between MPB and conventional subsurface dam and cutoff wall were compared to assess the applicability of different physical barrier. The numerical results show that the construction of MPB will increase the nitrate concentration and contaminated area in the aquifer. The prevention and control efficiency of MPB against SWI is positively correlated with the depth of the cutoff wall, reaching the highest efficiency at the minimum effective dam height, and the retreat distance of the saltwater wedge is positively correlated with the opening spacing. We found a non-monotonic relationship between the change in subsurface dam height and the extent of nitrate accumulation, with total nitrate mass and contaminated area increasing and then decreasing as the height of the subsurface dam increased. The degree of nitrate accumulation increased linearly with increasing the height of the cutoff wall and the opening spacing. Under certain conditions, MPB is 46%-53% and 16%-57% more efficient in preventing and controlling SWI than conventional subsurface dam and cutoff wall, respectively. However, MPB caused 14%-27% and 2%-12% more nitrate accumulation than subsurface dam and cutoff wall, respectively. The findings of this study are of great value for the protection of coastal groundwater resources and will help decision makers to select appropriate engineering measures and designs to reduce the accumulation of nitrate pollutants while improving the efficiency of SWI control.