Rice paddies are highly important agricultural soils in view of their relevance as major staple food provider in the world and their key role in the global carbon cycle, caused by special management practices. A soil chronosequence, consisting of paddy and upland soils, developed on reclaimed estuarine sediments in the Province of Zhejiang, China, was sampled to investigate the influence of duration of agricultural use (50 to 2000 yr) on soil composition. The uniform composition of the parent material provides the unique opportunity to compare the effects of different land management practices (paddy and non-paddy) on soil carbon dynamics and the origin of organic carbon (OC) in top- and subsoils, using 14C measurements by accelerator mass spectrometry (AMS). The total soil organic carbon (TOC) was split into chemically defined pools of different mobility, namely the acid- and water-soluble fulvic acids (FA), the alkali-soluble humic acids (HA), and insoluble humin fraction. The more mobile HA and FA fractions contain significantly more 14C than the corresponding TOC and humin, indicating a downward transport of OC in the subsoil. Plant roots with 14C concentrations up to 128% of the modern standard, found far below the plough pan, reveal plant roots and root exudates as other direct sources of subsoil OC in paddy soils.