Coastal eutrophication caused by excess nutrient inputs has increased worldwide. Of the exogenous nutrients sources to coastal ocean, benthic advective pathways, including large-scale submarine groundwater discharge (SGD) and centimeter-scale porewater exchange (PEX), remain the most uncertain relative to surface inputs such as rivers. In particular, the biogeochemical signatures and spatiotemporal variability of individual subsurface flows are poorly understood. Here, we present monthly field observations from January 2022 to April 2024 to assess seasonal dynamics of nutrient loading from different benthic advective processes and their ecological impacts in a chronically eutrophic semi-enclosed bay. We found that longer porewater residence times promoted ammonium and silicate accumulation, alongside the attenuation of nitrate and nitrite in the intertidal sandy aquifer. PEX dominated benthic advection, with enhanced water and solute fluxes during wet seasons driven by intensified hydrodynamic forcing and biological activity. Despite covering <5% of the bay area, SGD and PEX together derived 12–48% of dissolved nitrogen and 0.5–20% of dissolved phosphorus relative to riverine inputs, while PEX alone supplied >41% of exogenous silicate to the entire bay. By altering the magnitude and stoichiometry of nutrients, PEX and SGD exports likely exacerbate phosphorus deficiency. Partitioning the contributions of individual benthic advective pathways to long-term nutrient dynamics is key to mitigate coastal eutrophication.