Seawater and groundwater interactions shape the hydrogeochemical profile of mangrove aquifers, revealing how biogeochemical processes adapt to saline-freshwater mixing via the fluctuating patterns of key hydrochemical indicators and primary biogenic elements. This study, utilizing a multi-level monitoring profile spanning the entire submerged aquifer within a mangrove wetland, analyzed the spatiotemporal dynamics of DO, ORP, pH, alkalinity and biogenic elements (C, N, S). The results revealed that among the basic hydrochemical parameters, total alkalinity showed the most stable spatiotemporal distribution and was positively correlated with salinity. pH demonstrated a significant negative correlation with salinity, whereas the correlations of ORP and DO with salinity were not substantial. The discharge of terrestrial freshwater into the mangrove wetland is marked by hydrogeochemical reactions favoring the input of Mg2+ and DIC, with potential iron mineral precipitation within the aquifer. Spatial distribution of biogenic elements in the groundwater showed no apparent pattern across sampling periods. DOC concentrations ranged from 0.3 to 1.3 mmol/L. Three components of dissolved organic matter were identified using three-dimensional fluorescence spectroscopy, with high molecular weight components (C1 + C2) accounting for an average of 47 to 73 %. Both elevated DOC concentrations and high molecular weight component ratios were primarily found in shallow layers of dense mangrove areas, decreasing with depth. Concentrations of ammonia, nitrite, and nitrate varied dynamically, reflecting active biochemical processes in the shallow to mid-layers of the aquifer. Furthermore, sulfate and sulfide concentrations, ranging from 0 to 26 mmol/L and 0.4 to 576.8 μmol/L, respectively, underscore the interplay of biogeochemical reactions, especially sulfate reduction. These findings highlight valuable insights into the complex biogeochemical processes within mangrove aquifers and provide theoretical guidance for protecting the ecological health of mangrove wetlands.