Estuaries are hot spot for the preservation of terrestrial organic carbon(OC), whereas those small streams have long been underestimated. In this study, we compared the large river system represented by the Pearl River Estuary(PRE) with the small subtropical river systems represented by the Zhangjiang Estuary (ZJE) for their abilities in preserving terrestrial OC. The concentration and carbon stable isotope(δ¹³C) of short-chain and long-chain of fatty acids (ScFA & LcFA) are evaluated in PRE and ZJE as the representatives of labile and refractory organic matter respectively. The concentrations of ScFA in the PRE(~4000ug/g TOC) was higher than that in ZJK(~1500ug/g TOC), while LcFA concentrations (~400ug/g TOC) were much lower than those in the ZJK(~1500ug/g TOC). The higher LcFA in ZJE suggests a larger contribution of OC from the vascular plant in the small river system. The d13C values of branch chain fatty acids ranged from -30.61‰ to -23.33‰ along the main stream of PRE, which show similar distribution to ScFA (from -33.20‰ to -22.10‰). However, more depleted ¹³C was observed in LcFA (from -34.04‰ to -26.69‰) than ScFA and BrFA. The observed different isotopic distribution in ScFA and LcFA suggests their distinct origins: LcFA originates from the terrestrial vascular plant, while ScFA may be more influenced by the in situ phytoplankton production, which shows close interactions with the bacterial process in this large river system. In ZJE, the three categories of fatty acids shows more consistent ¹³C distributions to each other. This may imply the same origins of labile OC with those more refractory OC from terrestrial vascular plant, which also support the bacterial processes in this small river system. Our comparison between PRE and ZJE indicates that the OC preserved in the sediment of PRE was more influenced by in situ phytoplankton production in this large river system. While terrestrial vascular plant has more important contribution to the preserved OC in ZJE.