Biogeochemical reactions in an intertidal aquifer influences the submarine groundwater discharge (SGD) associated trace metal flux to the ocean. Tidal fluctuation greatly affects the physical mixing, and biogeochemical transformation of trace metals in the intertidal aquifer. This study presents the dynamics of trace metals (Fe, Mn, and Sr) and the production of Fe2+ in the salinity transition zone is discovered. The variations of Fe2+ are led by the shifts of both physical mixing and biogeochemical reaction during tidal fluctuation. The transformation from amorphous Fe(OH)3 to FeS is the main reason for the enrichment of Fe2+ in the zone with a salinity of 0.5-10. Mn behaves much less active than Fe in the intertidal aquifer due to the very limited Mn in the solid phase and the major driving force of Mn2+ variation is the physical mixing rather than geochemical reaction. Sr2+ behaves conservatively and shows a synchronous with salinity in the salinity transition zone. This study found that Fe2+ precipitates in a form not limited to Fe (hydro)oxides and the FeS minerals is the most possible form of precipitation in reduced aquifers. In that case, only a small part of Fe2+ discharges to the sea associated with SGD, but Mn2+ has a comparatively conservative property during the transport in the intertidal aquifer and majority of the Mn2+ originated from fresh groundwater will discharge with SGD in this study. The biogeochemical transformation pathways of Fe and Mn observed in this study provides insights into the cycles of Fe and Mn in an intertidal aquifer, which is of significance to accurately estimate the SGD derived Fe and Mn fluxes to the ocean.