Abstract There is evidence that sedimentary organic matter is prone to lateral transport under hydrodynamic processes before its final deposition on the seafloor, restricting the applicability of molecular proxies. In this study, we examine the abundances of marine and terrestrial biomarkers in bulk and the grain‐size fractionated samples (<20, 20–63, and >63 μm fractions) from surface sediments in the South Yellow Sea to decipher the spatial influences of hydrodynamic processes on the biomarker distributions and molecule‐proxies' applications. Our results show that spatial deviations between proxies‐derived sea surface temperature (SST; the ′ and TEX 86 indexes) and satellite‐derived annual mean SST may result from the lateral transportation of the alkenones and isoprenoid Glycerol Dialkyl Glycerol Tetraethers driven by dominated nearshore coastal currents. We propose a spatial‐SST correction approach to obtain more accurate SST information by removing the hydrodynamically introduced SST bias. Our investigations imply that hydrodynamic processes could be an important factor for controlling the spatial distribution of biomarkers in the ocean, further influencing the applications of biomarker‐based proxies for paleo‐environmental reconstruction. We suggest that this investigation would shed new light on the biogeochemical dynamics of sedimentary organic carbon pump in the shallow ocean, particularly in the passive continental marginal seas with strong hydrodynamic conditions.