This study examined the influence of preferential flow on salinity change, pore water flows, and solute transport reaction in variable saturation and variable density coastal aquifers. The 2-D unconfined aquifer model established was based on the finite element software COMSOL by coupling the dynamic and chemical processes together. The simulated results showed that both preferential flow and tide wave affect groundwater flow, leading to a more complicated mixing process than by only considering a single factor. Compared with the tidal force, the preferential flow was found to effectively reduce the length of seawater intrusion. The deeper the depth of preferential flow, the more significant the effect. Owing to this complex and dynamic process, nitrification mainly took place in the shallower zone adjacent to the coast, where oxic seawater and groundwater interact intensively. Denitrification, on the other hand, was dominant in the middle zone of the aquifer, where the oxygen was relatively lesser. Further quantitative analysis revealed an increase in the intensity of nitrification and dissolved oxygen inflow flux with preferential flow depth. This also led to a decrease in the nitrate removal efficiency. This phenomenon usually occurs on coasts where biological caves are abundant. The results also offer significant implications for designing engineering measures to mitigate saltwater intrusion and groundwater quality management in coastal zones.