Dissolved organic matter (DOM) in highly productive intertidal mangroves is an important carbon and nutrient source to the coastal ocean. In highly dynamic mangrove intertidal systems, both tidal pumping or geochemical factors can control DOM characteristics. The influence of groundwater flow on DOM properties and fluxes remains poorly understood. Here, we compared the concentrations, sources, and spectroscopic characteristics of DOM across a recharge‐discharge gradient. We used a three‐dimensional array sampling strategy to reduce spatial biases, groundwater monitoring to quantify tidally driven exchange, and spectrofluoroscopy to quantify DOM fluorescent components. The results showed that tidal hydrology played the key role driving groundwater DOM properties in both horizontal (i.e., from the mangrove to the sea) and vertical directions. Due to the high spatial heterogeneity of dissolved inorganic (DIC) and organic (DOC) carbon concentrations in mangrove groundwater, carbon outwelling showed a high degree of variability at the intertidal scale (54.8–234.8 μmol m−2 d−1 for DIC and 2.5–12.4 μmol m−2 d−1 for DOC). The contribution of terrestrial DOM gradually decreased toward the ocean, but the microbial contributions for recently produced autochthonous DOM increased. Deep groundwater received less terrestrial DOM and experienced anaerobic microbial mineralization, resulting in lower organic carbon than shallow groundwater. Greater variations in spectroscopic characteristics were found in shallow groundwater than in deep groundwater. Overall, tidally driven surface water‐groundwater interactions control the variability in DOM properties and how DOM contributes to carbon budgets and sequestration in mangrove groundwater.