Soils in the southern Ukraine have been reported to have lost 32% to 40%, or 51 to 71 t ha-1 of their original soil organic matter (SOM) pool between 1881-1981, mainly due to inappropriate soil management by collective farms during 1930-1981. In this period agricultural management was directed towards irresponsible expansion of arable fields and short-term yield increases. Modern, sustainable agricultural management is slowly being introduced. There is a need to assess to what extend such methods stabilize and build new SOM to support and increase fertility both in the short and long-term. This study investigates the influence of a modern crop rotation (onion-tomato-barley) on one field, which was tilled, fertilized, irrigated and harvested in response to the crops needs, on the dynamics of total organic carbon (TOC) and total nitrogen (TN) storage in the fertile topsoil of a Chernozem typical for southern Ukraine. Crop residue remained on the field. The results of three years (2007-2009) of quarterly monitoring of the key topsoil parameters TOC, TN, extractable mineral N (NH4+, NO3-, NO2-), pH, potential net N mineralisation (MIN) and nitrification (NITR) rates and physical characteristics (bulk density, soil texture) are discussed. Moderate (114 kg N ha-1 yr-1) and low (28 kg N ha-1 yr-1) N fertilizer applications together with adequate drip irrigation for onion and tomato and incorporation of plant residue did significantly change the C and N pools. Total organic carbon and TN contents of the topsoil horizon (0-74 cm) were found to increase by 20% (26.8 t C ha-1) and 38% (5.9 t N ha-1), respectively. Largest increases were measured in the surface layer (0-27 cm) with a 45% increase in TOC and a 36% increase in TN content. The largest average soil NH4+ content of the topsoil horizon (0-74 cm) was observed in 2009 under barley (154.9±41.3 kg N ha-1) and the maximum average NO3- content was 166.9±44.5 kg N ha-1 under tomato in 2008. Mineralisation and nitrification rates significantly varied between years and with season and were largest in the first year of the crop rotation (onion), 41.0±57.3 kg N ha-1 and 36.6±74.4 kg N ha-1 for MIN and NITR, respectively. The incorporation of plant residues and efficient N fertilizer applications within a crop rotation appeared to be effective in stabilizing the existing SOM and promoting SOM build-up.