Microcosm and field investigation were conducted to examine the effects of heavy metals on the decomposition and accumulation of organic carbon in contaminated Mersey estuarine floodplain, northwest England. The results show that inhibition of microbially mediated decomposition of organic matter occurred in the water-inundated soils. However, individual heavy metals had differential effects on the inhibition of soil organic matter decomposition with arsenic and copper being much stronger, as compared to other investigated heavy metals. The weak inhibitory effects of chromium on organic matter decomposition was due to the conversion of highly toxic Cr(VI) to less toxic Cr(III) under reducing conditions. Lead also had a weaker capacity to inhibit organic matter decomposition due to its low solubility. It was surprising that the same phenomenon was not clearly observed during the field examination. The inhibitory effects of heavy metals on soil organic matter decomposition could be curtained under field conditions. pH, Eh and EC played more important roles, as compared to soil-borne heavy metals, in affecting the soil carbon dynamics in the contaminated Mersey estuarine floodplain.