Temporal changes in the external forcing conditions of coastal aquifer systems, such as seasonal inland freshwater input, may disturb the balance between the ocean forces and freshwater hydraulic gradient. An increase or decrease in this imbalance may affect the stability of tide-induced upper saline plume (USP). In this study, we performed laboratory experiments and numerical simulations to investigate the influence of seasonal inland freshwater input on USP stability and the associated behavior of seawater intrusion (SWI) and submarine groundwater discharge (SGD). In contrast to previous studies, we found that USP was not always stable or unstable in the intertidal zone, but experienced a dynamically stable-unstable process as the seasonal inland freshwater input varied. The extent of SWI and SGD showed a dual response to the seasonal inland freshwater input. On one hand, seasonal fluctuation in inland freshwater input directly induced responsive changes in SWI and SGD; on the other hand, dynamic stability of the USP caused by the seasonal fluctuation resulted in an additional high-frequency fluctuation in the extent of SWI and SGD during the unstable flow. Moreover, the response of saline SGD and total SGD to the seasonal fluctuation in the inland freshwater input was nonlinear. This overall increased the SGD compared to the scenarios with a temporally constant inland freshwater input. Therefore, ignoring seasonal changes in the inland freshwater input may underestimate the amount of water exchanges across the aquifer-sea interface.