Abstract The paper presents the results of research on the relationship between topography of undulated morainic plateau of postglacial landscape and distribution of organic carbon stocks in soil toposequences. The mean value of the soil organic carbon stocks (SOCS) for Retisols/Luvisols (RT/LV) was statistically lower than for the Phaeozems/Gleysols (PH/GL) but for RT/LV a higher variation of SOCS in comparison to PH/GL was observed. On the basis of Pearson correlation coefficient, the cartographic depth to water (DTW), the topographic wetness index (TWI) and the saga wetness index (SWI) were the most strongly correlated with the SOCS from among 13 analysed topographic attributes. In addition, the DTW was more correlated with SOCS than other topographic variables. Moreover, the DTW based on the channel networks with 2 ha flow initiation thresholds better correlate with SOCS than DTW obtained on the basis of channel networks with 1 ha and 4 ha flow initiation thresholds. Using Stepwise multiple regression analysis (SMLR), we concluded that the topographic attributes controlling the soil water content and slope shape had most impact on SOCS of the undulated morainic plateau of agricultural ecosystem. In this landform, where the RT/LV and PH/GL soil sequences dominate, the SOCS can be estimated by the DTW, TWI and GC (general curvature) with an estimation error of 0.21 kg m−2. In view of the increasing availability of LiDAR data and power of GIS tools, the use of topographic metrics to assess spatial variability of soil properties will play an increasingly important role in the estimation of soil properties.