Floodplains are dynamic ecosystems wherein intensive farming can meet increased environmental concentrations and bioavailability of a number of trace elements. Therefore, the primary objective of this study was to investigate the partial digestion of selected trace elements in surficial soil samples (depth up to 40 cm) across a gradient of environmental conditions along the Ohře River and determining the elements of high priority, while also exploring their geographic variation. The established agrochemical testing of Czech soils provides a valuable resource to determine the geochemical differences of multi-element associations in cultivated areas (arable crops and hop fields) in periodically inundated areas in the catchment with a number of potential pollution sources. The topsoil samples were digested using the nitric acid (2 mol/L HNO3), analysed for trace elements (Be, Cd, Co, Cr, Cu, Ni, Pb, V, and Zn) using inductively coupled plasma mass spectrometry (ICP-MS) and atomic absorption spectroscopy (AAS), and for their total Hg content. Data (n = 130) were modelled against the sample location and cultivation using the log-ratio approach. The explanatory and inferential statistical tools (the Mantel's correlation test, PCA, MANOVA) adapted for compositions, combined with a simple spatial ranking and land-use information defined effective discriminating subcomposition (Cu–Hg–Ni) that were able to describe the changes of geochemical domains in floodplains and retained a decent representation (46%) of the entire compositional variability in our dataset. Mapping the Cu–Hg–Ni subcomposition using the RGB composite enabled to display the high-dimensional multivariate dataset with reduced information and enabled to discriminate spatial domains representing geochemical signatures related to changes in element inputs along the watercourse. The analysis of our results within the compositional framework showed a changing pattern of relative enrichment/depletion of the HNO3–extractable trace elements in which a regional contrast between groups of the chalcophile elements (Cu, Pb, Zn, and partly Cd), siderophile transition metals (Cr, Co, Ni, and V) and single elements (Hg, Be) was source-apportioned to the effect of point pollution sources (Hg, Ni, Cr, Co) as well as diffuse sources (Cu, Zn, Pb, Cd).