We investigated the fate of root and litter derived carbon in soil organic matter and dissolved organic matter in soil profiles, in order to explain mechanisms of short-term soil carbon storage. A time series of soil and soil solution samples was investigated at the field site of The Jena Experiment between 2002 and 2004. In addition to the main experiment with C3 plants, a C4 species (Amaranthus retroflexus L.) naturally labeled with ¹³C was grown on an extra plot. Changes in organic carbon concentration in soil and soil solution were combined with stable isotope measurements to follow the fate of plant carbon into the soil and soil solution. A split plot design with plant litter removal versus double litter input simulated differences in biomass input. After 2 years, the no litter and double litter treatment, respectively, showed an increase of 381 g C m^-2 and 263 g C m^-2 to 20 cm depth, while 71 g C m^-2 and 393 g C m^-2 were lost between 20 and 30 cm depth. The isotopic label in the top 5 cm indicated that 115 g C m^-2 and 156 g C m^-2 of soil organic carbon were derived from C4 plant material on the no litter and the double litter treatment, respectively. Without litter, this equals the total amount of 97 g C m^-2 that was newly stored in the same soil depth, whereas with double litter this clearly exceeded the stored amount of 75 g C m^-2. Our results indicate that litter input resulted in lower carbon storage and larger carbon losses and consequently accelerated turnover of soil organic carbon. Isotopic evidence showed that inherited soil organic carbon was replaced by fresh plant carbon near the soil surface. Our results suggest that primarily carbon released from soil organic matter, not newly introduced plant organic matter, was transported in the soil solution. However, the total flow of dissolved organic carbon was not sufficient to explain the observed carbon storage in deeper soil layers, and the existence of additional carbon uptake mechanisms is discussed.