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Sediment organic matter (SOM) differs in composition and function in different size fractions in relation to material and energy flows. The hydrodynamic effects on a lake's autochthonous (terrestrial plants) and allochthonous (microalgae, aquatic plants, and bacteria) inputs and transformation, and the components of SOM are still far from clear. To elucidate the SOM composition as driven by the hydrodynamic conditions associated with sedimentary grain size, we performed an ecosystem-level investigation in the shallow lake Izunuma, Japan, measuring source-specific fatty acids and the current velocity. High organic matter concentrations occurred in the finer fractions. Bacteria were dominant in the <32 μm fraction, microalgae were mainly present in the <32 and 63–125 μm fractions, aquatic plants appeared to be evenly distributed in all size fractions, and terrestrial plants mainly comprised the >125 μm fraction. Although the linear correlation between current velocity and sedimentary total organic carbon (TOC) was not statistically significant, the relationship between current velocity frequency and sedimentary TOC was significant. The highest Pearson coefficient occurred at a current velocity of 6 cm/s in sand. The relationship between allochthonous inputs and current velocity frequency was similar to that of TOC. Autochthonous organics had the greatest coefficient with two peaks at 4.5 and 8 cm/s. The threshold for sand resuspension varied with organic sources, while this phenomenon was absent in cohesive mud. Hydrodynamic forces affected the grain size of sediments and drove the gradient distribution of the SOM sources, which should be considered when managing freshwater lakes in light of future climate change. [ABSTRACT FROM AUTHOR]